Following my Raiden's family in Revengeance post, here's something akin to a fanfiction fix:
tldr: Rose and John are integral part of the story. Raiden has the chance to grow. There's an option to save Sam.
A long, self indulgent rewrite that fixes my problems with the game story. Enjoy!
Rose and John are a contact in Raiden's codec from day 1. Raiden can call them whenever he wants. Just like all codecs, not all discussions are important, but they flesh out the characters. It can be mundane, it can be a joke, it can be comforting or even an argument that expands over the story. Also Raiden can indeed pick up souvenirs for them.
Rose and John also have a couple in game unskippable codecs for the important scenes. So even the speedrunner player sees them. Mostly near key events.
Between the prologue and mission 1 Rose and John visit Raiden at the Maverick base in a cut scene. Raiden has a civilian body. They discuss what to do next and we see Raiden push for justice/revenge for what Desperado did to N'mani and his country. Rose may object, they could have a healthy argument. The argument can even be left unresolved for a few chapters, tension in a story is important.
The mission is to learn more about Desperado and sabotage them. Only later it becomes about taking them down as they are too dangerous.
In the story Raiden discussed with Rose that he'd go working for Boris at Maverick on the condition he wouldn't fight, but offer protection and mentorship. Now that things have changed, the missions involve fighting, their relationship could suffer a tear or it could show the love for each other can withstand this storm.
Gameplay wise Raiden is given more real stealth and non lethal options he can choose to use. Think of Deus Ex Human Revolution or Dishonored. He still kills a lot, but now it's the player's choice rather than the only option. Killing UGs means nothing, but killing cyborgs does, especially non-Desperado cyborgs such as cops. The point is whether Raiden chooses to be a hero or a living weapon, a question mgs2 and mgs4 asked.
Speaking of choices, what if this was a choice game? Well partly. Let me explain: it does matter if Raiden only kills top members of Desperado, if he also kills Desperado soldiers, if he also kills the Denver cops and if he kills Sam. Because the non lethal option opens this new possibility. Be a violent berserker and the story ends like Revengance: a lone vigilante, a terrorist, no Maverick and no family. Or be the necessary evil that keeps the greater evil at bay, but not become the villain aka show show basic empathy and mercy damn it!: there's a new ending unlocked. Not killing the cops and most soldiers also dismantles Sam's argument.
If Raiden doesn't get in trouble with the Denver police, aka he avoids them or only disarms them then he isn't considered a real threat. His business with Desperado is purely PMC against PMC and it's oustide jurisdiction as Raiden didn't hurt anyone. Rose and John still have to go hide in New Zealand for safety, but it's only temporary and this time Maverick covers for that. After Desperado is taken out, they would be safe to return home.
I was thinking the reason why Raiden goes after Desperado in Denver could be that in Mexico pr earlier Desperado threathens to hurt his family if he persued his mission. Raiden knows Desperado would go after this family regardless, so he organizes their safe trip, then goes after Desperado because they crossed a whole bunch of lines.
To still get the Jack the ripper moment Monsoon could cut Raiden's contacts after arguing with Rose. Desperado could isolate Raiden till the point of breaking, swarming him with enemies and poking at his mind. Raiden breaks, showing he does depend on his family and friends as a support line, but he also shows restraint as he only unleashes this persona on Monsoon and later Sundowner.
Raiden decides to keep ripper mode available. Afterall something broke inside of him and the ripper is what is keeping him alive right now. This is a ptsd/did response to high stress situations. But also the start of merging/healing as Raiden didn't lose control, he chose to allow Jack to take over to win the battle. They coexist now and Raiden is in charge unless he's in great trouble. Raiden must not abuse of this mode as 1 it's damaging his body permanently and 2 it slowly corrodes his mind.
After killing Monsoon, the codec connection is restored and we get to hear his friends and family again. This is the climax of the argument, weather or not if Raiden is a hero or a vigilante.
If Raiden wasn't a berserker and he chooses to open up about the ripper personality to Rose then we see she still supports him as he's doing his best out of a bad situation to save those kids. Because they are what Raiden once was and he cannot allow them the same fate. Rose understands, she knows his past.
Raiden's actions should have an effect on John who in mgs4 considered his dad a hero. Let's keep being a hero for him and not a monster who kills for the pleasure of it even when other options were available. Raiden might be physically away from him, but keeping in contact and acting as a good role model is important for John's development. (yes I'm taking this from Dishonored Corvo-Emily dynamic).
It's important to remind the player what Raiden if fighting for the people he loves and cares about. For friends that got killed or hurt like N'mani, for the kids Desperado harvested, for keeping his family safe .
After Sundowner the game rushes towards the ending, weather Raiden kept a good relationship with his family will be important after the Armstrong fight.
Now about the Sam battle. Keeping the dramatics and ridiculous over the top action of Revengance, if Raiden was a hero he wouldn't kill Sam, but he'd get close. Raiden defeats Sam after a very difficult fight, disarms him, cuts his cyborg arm (a nod to the prologue, now reversed), then pushes him to the ground and plants his sword right next to Sam's head, missing on purpose. Sam can't believe it, he starts laughing. Raiden punches him in the face, knocking him out. He then takes Sam's sword for safekeeping and to make sure Sam loses it. As the sword is locked, Blade Wolf is taked to keep it. The two get to Sunny's base. Raiden sends Maverick a message to capture Sam.
Notice how Raiden could have killed Sam if he leaned on his ripper side more. He uses it to defeat Sam, but decades to stop it before the killing blow. Also nothing says "I'm better than you" than denying your rival a cool death and humiliating them. Raiden didn't deny his sword its purpose, he denied himself being a weapon just because someone wanted him to be one.
Raiden fights Armstrong as usual, his sword breaks and we get the cool scene with Blade Wolf throwing him Sam's sword with Sam's codec calling him this time instead of a recording: Sam planned this, he tested whether Raiden could possibly defeat Armstrong and not get fooled by his propaganda. Now with Sam's sword Raiden kills Armstrong and crushes his heart. In the hero version Raiden would reply to Armstrong's final words, saying they are not alike and negating his philosophy.
In the good ending we see Raiden, Rose and John reunited. Raiden takes a long vacation from work. Maybe killing Armstrong didn't shake the foundation of the corrupt government, but not killing him would have represented a danger for the people he loves/cares for.
Because the long distance relationship is getting hard, Boris and Rose talk about Rose getting a job at Maverick to stay closer to Raiden. It would also be cool to have John interact with Sunny, afterall these are the kids Raiden cares about.
And to close it, Sam joins Maverick too. New arm, new sword (Raiden gets to keep the old one). They are now colleagues. Sam can cover for Raiden in missions so he wouldn't be away for months. And we get the bickering dynamic we all love between Sam and Raiden as good guys kicking rival PMCs ass.
It is a much more hopeful ending, it ties the old games and Raiden's progression and it shows character growth.
Together with Maverick Raiden and team expand specifically into security and branching into espionage targeting organizations like Desperado, so they can sabotage them before they get as big.
The end. Thank you for reading my unedited ramble! <3 I needed to get this out of my system.