Trying to untangle the problems I have with IDW1's way of writing the Autobots vs. Decepticons in terms of morality and all I have is a rough cluster of bullet points rather than a coherent thesis, but the bullet points are along the lines of:
From a genre perspective, I believe the Autobots could/would be "just as bad" as the Decepticons simply because it's written as a gritty/realistic military fiction, and in real life there is no army that never commits war crimes or abuses the other faction under the justification of "they're the bad guys/they're the ones who ruined society/etc"
However, I also think that the narrative/writers tried to have their cake and eat it too with the Autobots, where they simultaneously write them as committing heinous war crimes but also as the objectively better good guys
Which is bad because a lot of the times the way the Autobot "war crimes" exist doesn't feel like the way war crimes would feasibly exist under the code of ethics, worldbuilding, and leadership they have. Biggest culprit being JRO and writing The New Institute as still happening under Optimus' rule in secret even though 1. this makes Optimus look either stupid or ignorant in a way that he's not established to be or 2. this splits the Autobots into such divided internal factions morally that it's hard to imagine that the New Institute both went undiscovered AND there were never interpersonal conflicts among these different Autobots with different morality. I could go on and on about this specific point but this bullet point is already too long.
Even when the Autobots are textually stated to be just as bad as the Decepticons, it's always in a vague, unspecified way (the Aequitas files, what Tyrest saw in the trials that turned him into a neutral) and never in a way that's defined with explicit acts, explicit perpetrators, or rationales for how it was allowed to exist. We are entirely "told, not shown" that the Autobots are allegedly just as bad as the Decepticons, but it's never in a way that's revealed to the universe at large, never in a way where specific hero Autobots are actually held accountable or punished for what happens.
It also feels like a cover-up for flimsy writing to have these unspecified files/trials say "the Autobots are totally just as bad as the Decepticons" as an excuse to not actually specify what they did that was "just as bad" as something like, say, Grindcore, which was literally modeled after concentration camps. Like I'm sorry but even as a morally gray Autobots/flawed IDW Optimus enjoyer, there's no fucking in-character and rational way that you could tell me "yeah Optimus would totally endorse and allow concentration camps for Decepticons to be run." Which ties back to the second bullet point where I said that the writers try to make the Autobots just as bad, but not in a way that actually makes sense for the organization as it's run.
In general the writers want the Autobots to be just as bad as the Decepticons, except they (including notorious Megatron apologist JRO) seemingly can't let go of the over-the-top Decepticon monstrosity plotlines where they continuously have ridiculous shit like concentration camps, divisions solely dedicated to organic planetary genocide (Phase Sixers), an internal Stazi force dedicated solely to eradicating traitors to the cause (the DJD), multiple mad scientists that either partially or fully destroy whole planets in the name of their experiments, so on and so forth.... and then the best you can give me on the Autobot side is like, War Crimes Georg Prowl, Mesothulas (who was acting on Prowl's behest so that's technically a subset of Prowl's crimes), and the Wreckers.
Like really the faction morality in IDW1 seems to be a mix of authors wanting to have their cake and eat it too re: "the Autobots are morally gray BUT they're actually still the best heroes ever" OR just going "erm yeah the Autobots are just as bad um, throw in some unspecified war crimes that will never have a meaningful narrative impact ever" or "let's have some random Autobot or two be an absolute mass murderer torturing brainwashing evil freak and have them fill out the atrocity quota for the whole faction so that we can call the Autobots 'morally gray' even though the 'moral grayness' is entirely pinned on a handful of token evil Autobots."
It's very annoying because I COULD believe that the Autobots are just as bad as the Decepticons and I think there could've existed a version of IDW1 where this was written in a believable way, it's just that that didn't actually happen and people give the story credit (or get mad at it) for supposed political implications that weren't actually intelligently put in and were more just accidents or aborted plot ideas at best.
