The Kup Mind Link
The mind link plotline with Kup from AHM 15 marks the beginning of Prowl's character assassination in the IDW1 comics. It's the first morally dubious thing he's shown doing and he's portrayed very differently from how he was before this. When examining it as a continuation of Spotlight: Kup and the related plot threads, the underlying problems with how Prowl was written become very apparent.
Spotlight: Kup
In Spotlight: Kup, Springer sent the crew of the Ark 17 to rescue Kup. Despite not being equipped to handle the complicated situation, Springer pushed to do the mission anyway and got all but one of them killed.
Springer is pretty callous about the situation. He shows up angry that Kup hasn't been rescued yet and acts like what he's doing matters more when the sole survivor of a mission he ordered calls him out on his mismanagement. Siren is rightfully mad at him over this.
Something that doesn't really come up much after this is Kup basically mentoring everyone and being well liked for it. This only really stuck around for Springer, but it's why Siren finds dying to him especially bad. Springer emphasizes this as part of why they have to keep trying to save him, as well as why anyone who thinks they should stop just doesn't care enough.
Springer's insults to Prowl aren't actually true. He's just lashing out because he doesn't want to let Kup go. Prowl got the worst of it because he's pushing the most. Prowl's not saying those things because he doesn't care about Kup, he's saying it because the lives of the Autobots Springer is throwing away should matter enough to stop. Kup's life shouldn't be worth more than anyone else's.
Springer's lack of respect for Prowl's authority is because Prowl doesn't have any. He's not part of Autobot High Command, he's only in charge of the team on Earth. Springer likely outranks him, same as Hot Rod. Prowl can't actually do anything about Springer besides talk him down or report him to Optimus. He only knows what Springer's doing because Optimus set up stuff to keep commanding the Autobots on Earth. Prowl might be overreaching by using it unless Optimus asked him to check on things for him.
Springer's assumption that Optimus would support him is wishful thinking and doesn't fit with the characterization he had at the time. Prowl's reluctance is probably because he'd rather Springer came to his senses on his own. He was reluctant to call Optimus to Earth before he was sure the situation warranted it. Getting him personally involved in Springer's botched mission would take his attention away from the situation on Earth even if he didn't support Springer.
Perceptor manages to get through to Springer, who calms down and is ready to let Kup go. So of course this is when Trailbreaker shows up and pretty much singlehandedly rescues Kup.
'Oops, I guess I shouldn't have sent all those people to die and been such a rude jerk earlier. A bit of patience would've saved Kup without any casualties.' He thankfully has some awareness that he messed up, but that's not enough. The least he can do is apologize for how he acted.
The whole story makes it very, very clear that Springer is in the wrong. Multiple people call him out on what he did, he himself admits he was wrong and the story ends with him feeling regret about his actions. The plot hook wasn't just what would happen with Kup, but also Springer answering for what he did.
AHM 15
Springer punched Prowl before even asking why Kup and Perceptor weren't where he thought they'd be. He's jumping to violence before he even has a clear idea of what's going on, which is a bad way to respond to situations. It's immediate, unnecessary escalation that can easily cause problems that could've been avoided. When applied to the war, this is the kind of thing that gets people killed. We even get an example of this earlier in AHM. Ironhide was convinced that Mirage betrayed the Autobots. He decked Prowl for trying to talk him down, and then beat up Mirage.
Prowl doing shady things behind the scenes doesn't retroactively justify Springer physically assaulting him. What would Springer have done if Prowl didn't know where Kup was or didn't have anything to do with what was going on? Despite the Prowl bashing, the way Springer is shown looming menacingly over Prowl with his energon soaked fist is at least letting Prowl have a point about Springer's violence. He's a thug in that moment, not a hero.
This story is where Prowl first gets retconned into being part of Autobot High Command, or something to that effect. As covered in Spotlight: Kup, his authority was pretty limited up to this point. Prowl doesn't seem to be in charge of Kimia, so much as he now has the authority to move people around bases and assign missions.
Prowl has to ask Springer how familiar he is with Kimia, and Springer has to explain all the weird stuff the Wreckers had to test from there. This means that Prowl isn't involved enough with Kimia or the Wreckers to know all the details of what they do together. Prowl's later comparison of keeping the mind link secret from Springer to Springer not sharing the unpleasant details about the Wreckers also comes off like Prowl doesn't know the full details of what goes on with them.
Prowl's new characterization appears to be based on Springer's insults to him back in Spotlight: Kup. There are several moments where Prowl's narration basically goes 'Springer was right' either in response to comments Springer is making about Prowl or about things he said back in Spotlight: Kup. Stuff like Springer characterizing him as an uncaring jerk, Prowl considering getting Kimia to weaponize Kup's radiation sickness and the idea that Prowl carefully calculates even the things he says to people.
It's not just Prowl but also the idea that Optimus would've supported Springer's mission to rescue Kup, even with all the deaths. The narrative is turning itself inside out trying to make Springer right about things when he really shouldn't be. Even the High Command Prowl thing is like a misreading of Springer's sarcastic comment about Prowl not being in High Command. The narrative 180 completely misses the point of the story it's supposed to be continuing.
This is the start of the trend of painting Prowl as obsessed with winning the war, but it's pretty clear in context that "winning" means getting as many people to survive until it comes to an end. The Decepticons are trying to systematically wipe out life on every planet they take over and fully intend to do the same to the Autobots. AHM is all about the Decepticons trying to do this.
The reasoning for the mind link is that too many Autobots like Springer are going off to do things that are getting people killed. Prowl can't get them to listen and follow strategies meant to keep people alive, so he's taking drastic measures to fix the problem. The problem he's trying to fix needs to be fixed or else everyone will die.
Springer can't even take sole responsibility for his actions even after Prowl corrects him about it. This is worse than where he was at the end of Spotlight: Kup, where he at least admitted to it when talking to Trailbreaker. Seems a bit hypocritical to give Prowl so much trouble and then just refuse to acknowledge a mistake he already knows about. The payoff to scenes like this should've been for Springer to have to confront the flaws and mistakes he's been denying as part of a character arc. We never really get that.
This is also the beginning of a dichotomy where the "real" Autobots are reckless and driven by emotion, while people like Prowl are bad because they're logical and therefore emotionless. Prowl's narration as a whole pushes this idea with how hard it tries to make Prowl seem cold and unfeeling about what he does.
Due to Prowl getting set up as a strawman, the implication seems to be that there is something unethical and evil about following logic over emotion, in addition to the idea that reason and having emotions are somehow mutually exclusive. After all, that's what sets the heroes apart from the villains. Not just the Autobots and Decepticons, but also characters like Prowl and Springer.
This becomes more overt in later stories, where characters outright question Prowl's status as an Autobot or claim he'd fit better as a Decepticon because his logic driven actions are unethical. Narratives like that are anti intellectual, as well as ableist. Being the strategist or the guy that hits things doesn't determine a character's morality. The dynamics at play here fall into stereotypes where the often autistic or otherwise neurodivergent coded characters are somehow less empathetic and moral because of those traits.
The part claiming the Decepticons are more logical and organized than the Autobots doesn't really match what we're shown, either. Aside from the ones already referenced, there's Starscream's coup in the Furman run, all those Decepticons who supported him even after it failed, his coup in AHM with a different set of Decepticons, Sixshot, Thundercracker and Ramjet in his spotlight. It gets even more ridiculous when you look past AHM, where there's a whole plotline where Megatron has to manipulate the Decepticons into supporting him again and some of them still don't. Then there's Shockwave, Overlord and the mess on the asteroid. Megatron rules through fear and created an environment where all but his more fervent loyalists want to ditch him either for a power grab or because they're fed up with how he treats them.
Megatron has been pretty hot headed up to this point and even says this earlier in AHM:
In AHM, the Decepticons primarily define themselves as warriors who take what they want. Megatron encouraged this mindset and leads them through force, not logic. That's a tool for people like Starscream, who disagrees with Megatron's methods and is trying to usurp him over it. This conflict continues into RID, where Starscream doesn't want the war to restart and is trying to gain leadership of Cybertron through cunning instead of the force Megatron relied on.
This is similar to part of Prowl's narration shortly before his comment about the Decepticons:
From this point on, both Megatron and Optimus have similar flaws of driving the war through their unwillingness to do things any way other than their own, even when it makes no strategic sense. The Decepticons aren't really doing any better on this.
The setup around the mind link doesn't even make sense. Prowl is getting retconned into having more authority so he has the resources to do this, but more authority would mean he should have an easier time disciplining the people who don't follow his orders. That would get in the way of making Prowl the bad guy, so the story just ignores that.
Autobots in the Furman run weren't facing appropriate consequences for their actions because other things kept taking priority, the narrative wasn't fully acknowledging the problem with their actions and they somehow didn't get anyone killed. It also toned down on that, doing a better job with Hot Rod and Grimlock than it did with Ratchet and Ironhide.
Instead of improving past weak points in the writing, the entire Autobot chain of command gets retroactively broken by establishing that they're actively sabotaging themselves on a regular basis. Optimus is now an enabler of these problems instead of a good leader who reigns people in when he can and the few people with enough sense to notice the problem are being ignored.
Why would Optimus appoint someone to a job they're prevented from doing? Why is it not a problem that Optimus can't enforce his own chain of command so that the people in charge of giving competent strategies can keep people alive? Why are those people the bad guys and not the ones actually getting people killed by not listening?
Another problem with this is how inconsistent it is with the rest of AHM. This version of Prowl makes no sense when directly compared to the one talking to Kup in AHM 6:
The Autobots and Optimus recklessly getting people killed on a regular basis with no thought to the consequences also conflicts with AHM 13, where Ironhide's friendship with Optimus began when Optimus was willing to listen to and learn from Ironhide's criticisms about how to better lead people to avoid unnecessary deaths.
The Autobots were a lot more conscious and remorseful about that sort of thing when they were stranded on Cybertron, but now suddenly they don't care how many people die on a poorly planned rescue mission? How is that supposed to be more ethical than using Kup as a mouthpiece to convince Autobots to stop getting people killed?
Infestation
Infestation was one of the generally disliked crossover comics. It's easy to ignore but it's also one of the few times the Kup mind link came up.
The gist of the plot is that there's a zombie plague hivemind that can infect both humans and Cybertronians. Its main representative and the villain of the crossover is Britt. Galvatron's ship ran afoul of them and crashed on Earth. It's not a good look for Galvatron and Optimus fights him. Skywatch is also there because this is during their alliance with the Autobots. The conflict with Galvatron in the midst of a zombie apocalypse takes a lot more page time than it really should.
Kup starts to remember the zombies from Tsiehchi, drops his cygar in his panic and starts spiraling. AHM 15 established that the cygar contained a synthetic version of the radiation he'd been exposed to and would help keep him from regressing to the state he was in when they rescued him. Kup gives away Britt's disguise, causing her to stab and infect him. The information Britt gains from this allows her to create a portal to past Cybertron. The Autobots initially try to destroy it with missiles, but she creates a forcefield based on the one they used to quarantine the area. That's when Prowl uses the mind link to contact Kup, since he's the only chance they have left.
It's easy to say Prowl just used Kup and threw him away when recounting the events in SOTW, but that's just not how it happened. Prowl used the mind link to restore Kup's mind and communicate with him, not control him. He explained what he was doing to Kup, what was happening to him and what they needed him to do. Optimus, Galvatron and Bumblebee were all there and participating in this too.
Circumstances didn't really give Kup much of an option besides what he did if he wanted to do something about the zombie situation, especially since he was a zombie himself. Still, he was clearly aware of himself and acted on his own power when he did it.
Prowl is the most visibly distraught over what happened to Kup. You can infer Optimus is too, but no one else really gets a reaction shot. Infestation isn't exactly a good story, but Kup's part is worth reworking into something better. It's about as good of a resolution to the mind link plotline as could be expected. The explanation and use for it are better than the original premise and Prowl is allowed to care about people. There really wasn't any reason to bring it back or erase Kup's memories so he could re-experience his trauma. It was handled better here than in SOTW.
Sins of the Wreckers
In Sins of the Wreckers, the mind link is first hinted at with Kup experiencing blackouts. Arcee is immediately suspicious this is connected to Prowl, but it comes off more like she's drawing on the writer's knowledge of the plot. She doesn't have any reason to suspect Prowl has anything to do with it until Kup figures out the code to Prowl's office.
The mind link ends up being revealed when Prowl takes over Kup to contact the Wreckers directly. This involves a visual effect with glowing eyes and a laser chevron to make it clear that Prowl is in control. Prowl's voice is presumably also in effect. It was probably supposed to look cool and dramatic but just ends up highlighting how absurd and inconsistent the mind link plotline really is.
This whole scene comes off like it's designed to make Prowl look as unsympathetic as possible to justify hating on him. Making it sound like he used Kup and doesn't care about the cost because he saved the world. When you have context for what actually happened, the inaccuracies and the way the story tries to retcon away any sign that Prowl isn't as bad as it wants you to think he is just feels disingenuous.
Erasing Kup's agency in his sacrifice, Prowl's grief over it and that Kup was basically as good as dead before he did it only really serves the narrative that's been character assassinating Prowl since AHM 15. Springer and Arcee being the ones to moralize about this makes it even worse with how the terrible things they've done pretty much get glossed over.
This is Sins of the Wreckers and yet all the people Springer killed to save Kup are just a footnote. It's completely buried under the mind link plotline and the story's fixation on making Prowl the Worst Autobot Ever. This whole plot thread started with Springer getting mad at Prowl for trying to talk him down from getting more people killed. The most that's given is that it's what Springer feels guilty about when put through Impetus. Springer feeling guilty isn't a resolution, especially when he keeps dodging responsibility when it comes up. The narrative seemingly just brings it up to remind people that it's choosing not to actually address it.
Kup's trauma and recovery is just a footnote too. Just compare this to Infestation. Kup just gets a brief moment to cope with the revelation and then it's back to hating on Prowl. All he gets after this is telling Prowl how much everyone hates him in his message later. This whole story arc isn't really about him.
It doesn't really make sense for Prowl to bring up the people Kup killed when it wasn't necessary. He covered it up before Springer even asked because they both felt that it was best he never find out. Kup shouldn't even be aware of that conversation.
The rules around the mind link make no sense. The other uses within Sins of the Wreckers establish that Kup needs to black out for it, but he's aware in this case so he can hear the conversation. The last use after this also has him message Prowl while knocked unconscious, which shouldn't be possible either. The only part that makes sense is when Kup knew the code to Prowl's office.
Aside from that, nothing we see the mind link do in SOTW is consistent with what it was allegedly for. How exactly is Prowl supposed to get people to listen to his strategies through Kup if Kup keeps passing out or noticeably isn't acting like himself? No one is supposed to notice, including Kup. The super showy talking through Kup effect shouldn't be there either.
Guzzle
The other thread stemming from Spotlight: Kup is Guzzle. His backstory establishes that most of his old platoon died trying to save Kup. Despite the coverup, he's aware of how they died.
By the end of LSOTW, he's extremely violent to the point that Impactor tries to reign him in. That's why he starts SOTW locked up. For SOTW, he's little more than a violent loose canon everyone else is trying to steer in a useful direction. The payoff to his storyline is that he holds Prowl and Kup at gunpoint once they get out of the noisemaze.
Prowl is basically just lumped into Guzzle's grudge for narrative tension around his rescue and another chance to go on about how terrible he is. Despite Springer being the reason all those people died trying to save Kup, he doesn't get mentioned at all. He's busy heroically sacrificing himself to stop Tarantulas and getting praised as a beloved hero. There's no room in the story to criticize him.
Guzzle gets some compassion from Verity and that's it. He doesn't get to finish talking before Impactor kills him. Springer's terrible mission planning got his friends killed, joining the Wreckers caused him to spiral into violence, they bring him on the mission despite clearly being a liability and then he gets killed when he inevitably becomes a problem.
Guzzle is a pretty clear example of the issues with Springer and the Wreckers, but the story doesn't really do anything with that. He's one of the few living characters harmed by Springer's rescue mission, which should've led to confronting Springer with the consequences of his actions. Springer recruiting him into the Wreckers and the effect that had on him was also an opportunity to discuss the toxic culture the Wreckers have that turns people into war criminals.
Siren survived the mission and was pretty mad at Springer back in Spotlight: Kup. He easily could've been brought back as part of this plotline, which would've opened up more options on what to do with Guzzle.
Conclusion
The mind link plotline is just a mess of bad writing. It's inconsistent, vilifies Prowl for bad reasons and undermines the narrative themes of the story it's supposed to be continuing.
Springer started out as a high ranking Autobot who got people under his command killed because he couldn't put their lives ahead of Kup. By the end of the Wreckers trilogy, he's an untouchable paragon whose heroic qualities are meant to inspire people to do better, and yet he never had to get any character development to address his own flaws. They just matter less and less until all that's left is people's idolization of him.
For all the hate Prowl gets, he's the only one who seems to care about what Springer did, and he seems to care more about saving lives than the other Autobots. The whole premise of the mind link is that Autobots are so entrenched in self-destructive ideals that they apparently don't reflect on the deaths their actions cause, the preventability of those deaths or the value in listening to strategies meant to avoid them.
The Autobots that died trying to rescue Kup didn't want to die in that mission. They didn't need to die to save him and dying didn't get the mission any closer to succeeding. Why is it more heroic to send all those people to die out of negligent mission planning over one person than to refuse to put more lives in danger? Why is Prowl somehow less empathetic for quantifying the potential death toll and trying to avoid it, when everyone else apparently doesn't care how many people die as long as they get to feel good and heroic in the short term? Why is Prowl the only one blamed for deaths attributed to his actions and not people like Springer or Arcee?
Instead of bashing Prowl, the followup could've had Springer try to get Kup's mind rebuilt. If it's pretender tech you can still do a mind link plotline without it being some nefarious way to use Kup. Pretenders already had a mind link feature built in, and the link could be what's holding Kup's mind together. What makes the most sense here would be for Springer to do it, which could invite existential questions of how much of Kup is the real him and how much is Springer's idealized memory of him.
If you really want Prowl to be linked to Kup, it can be with Springer's knowledge, maybe because he was worried being a Wrecker put him in too much danger. Prowl cared about Kup too, he just had the sense not to get people killed over it. Without making it a secret mastermind thing, you could explore how Prowl getting shadowplayed, mindcontrolled and shoved into a combiner would affect Kup.
Overall, it should be more about what serves bringing Kup back in a state that continues the original plot thread about Springer having to deal with what he did. That means giving Kup agency in confronting what happened to him and how he feels about it. Prowl's not really necessary for that.