Not saying genocide is a good idea, but I'm not seeing any better ones at this point. Marley's been made out to be total monsters (and the rest of the world isn't shown to be much better). The ancient Eldians were total monsters, the modern-day Eldians aren't all that great either. Every group in the series is just begging to get shoved into ovens, so which one am I supposed to pick (and does it even matter at this point?)
It no longer matters. This series does not have a protagonist, nor does it have an antagonist. Everyone and everything in it has become pointless. I don't feel connected to any of the characters, nor does their 'struggle' matters to me. Its been all inflated bullshit. There are also ways to destory marley without genocide, and I mention them below.
Here's the thing with Eren's genocide plan. When you look at Eren's character from start to finish, this outcome was entirely possible and made complete sense. He wanted to kill them all, them being the titans, and now that he's done that, he can't stop killing, and has become the very thing he hates. That's an understandable character arc, and a unique ending for AoT's original genre. If we're going by the first few arcs of the series, this is not a problem
The problem is that by the time of the Marleyan arc everything has just become too complicated, and convoluted for this to be executed properly. There's just too many plot holes, inconsistencies, questions, and world-building issues for a straight forward ending like this to work out. There's way too many outside factors at this point. Where do the PATHs system, Ymir, and everything fit into this? Simply put, they don't.
Again, it's not the idea, but just how fucking terrible the execution of that idea has been.
If I had to rewrite this plot, and had to include his genocide plan, I would just simply have Eren become so far gone that he can't stop killing, and perceive everything outside the Walls as the threat to his life, and his friends. The outside world that he longed to see when he was a kid is now nothing more, but another titan for him to deal with. Hell, if I was forced to include the KoM, they would at least make more sense here, because after we have the Paradiser over throw them, we can have Eren decide that there's no point in trusting Outsiders, and that everyone else outside the Walls needs to be destroyed. It doesn't matter that he has never met them, or the fact that they're good people, he doesn't care. He's too far off his rocker to stop.
There's no PATHs system, or any other shit like that. No Ymir, no Historia baby, no Eldians, and if I was forced to include the KoM, I'd just have them be the first outside civilization the Paradisers encountered, and they just happen to be evil. Basically, none of the crazy magical shit we have to deal with now. I'd would just keep it as straight forward and simple as possible.
It's not very good, but if I absolutely had to keep this end goal the same, this is what I would do.
Eren's genocide plan doesn't make much sense at all in the current iteration of the story. It was all 'freedom freedom' and his motivations were basically shrouded, along with his emotions. Making there really no build up to this point. It was never shocking as people predicted this forever ago. I don't know why he thinks its a total shocker. It was because him being shrouded in mystery could only mean something terrible along with the way Eren was behaving, but there's really nothing backing this behavior. He could blow up all the industry, military and all of that of the mainland. Just wreck it, bring the Titans back and restore the walls. Its actually pretty simple, it would take them decades and decades to rebuild. Also if you destroy all the governments, the whole continent will be in complete disarray. You just don't go back to conquer it. You've completely cut off all the heads of the snake: military, industrial, political. You leave the farms and the other civilian infrastructure alone. You basically neuter their capacity to wage war and competent leadership. Countries typically don't come back from that and its highly likely Marley itself will de-evolve into civil war. Genocide is completely unnecessary.
Eren basically has the dream: Unstoppable forces to destabilize entire countries while limiting civilian casualties, yet he decides to use it to genocide. My question: Why? You throw the main continent into chaos, with different leadership factions vying for control, too busy to consolidate their own power than care about an offensive. Its an extremely logical, even-headed maneuver. You can also exploit that chaos by offering support to the warring factions. Basically, ensuring Marley is a state of eternal civil war and can never, ever possibly unify for centuries. Pass down the Power of the First Titan to Non-royalty and you literally have a God-King to which Marley can never touch. Re-do the programming so it can only be activated for defensive reasons. You punish Marley, preserve Eldia and don't have to genocide anyone.
"They'll always hate us" isn't necessarily true. And even if it is, you have an arms stand off. Its just really...stupid. "I'm genociding to stop genocide and they're evil, even though this is clearly the same logic they use against us. I am 100% better." This argument is hilariously fucking incompetent. Eren is arguably unstoppable at this point and without some bullshit he's going to extinguish all life for really no good reason. Without a desux ex machina, I don't see how he's stoppable.
You could have established that the constant bloodshed Eren experienced, the deluge of memories (I'd keep the Attack Titan memories, but not through time and space, just the memories of the holders), his alienation only experiencing hatred, his friends becoming distant from him, becoming addicted to the adrenaline rush of battle and conflict, and being unable to stop. He becomes insane and less and less rational. Being so young, exposed to such extreme emotions and become a monster who has experienced centuries of hate and it just overwhelms him. Maybe during that flashback it triggered an Attack Titan user's memory of being slowly tortured to death and it starts to mentally break Eren, become less and less sure of who he is.
The main conflict of the manga becomes between Eren, Mikasa and Armin vs. Everyone trying to use him as a tool of war and them trying to keep someone they love sane. Its extremely emotional, because we've seen them as kids and his father basically cursed him with this insatiable bloodlust. Its not even Eren's fault, it goes with the theme that its this cruel world. The focus would be completely away from politics. KoM would barely be there, but the emotional tension would be between this changing Eren, who is struggle to control his burdening bloodlust and his friends. The political angle comes from the brass who love using Eren as a living weapon and are only happy to exploit his growing bloodshed for their own ends. Eren wouldn't be a political outcast, he'd be an 'ally' of the monarchy, their dog of war. Eren struggles between his own agency, his desire for freedom for his people being pure and his desire for an eternal war being the man conflict. It'd be Man vs. Nature. The ultimate feeling of compassion before his people vs. the unyielding rage of a monster created by the world itself, callous and indifferent to life, guilty or innocent.
I'd portray Eren more as a victim, Mikasa would take over protagonist duties after the basement. We're familiar with her and can empathize and sympathize at how someone she loves is being exploited. The problem is people start viewing her to be a freak once the truth about her nature is revealed, drastically reducing her influence. Eren would be an anti-hero, maybe you even have a twist and have Levi or Hange be the antagonists, wanting to use Eren for their own ends, not caring the psychological, physical and mental tolls that he takes. They view him less and less of a human being and more as a tool. Maybe have Eren and Historia have a relationship, but because of what he is, he is never allowed to see her again, further driving him mad. Especially add to his agony knowing that he's a father and he can never, ever see his child. Or the woman he loves ever again, under the threat of his, Mikasa and Armin's execution.
The problem is he's bundled down everything with so much unnecessary shit and created mystery boxes for no reason and uses flashbacks to justify exposition. Then there's the 'big events' that don't even matter. (Annie being Crystalized, Historia and Eren's relationship, Historia's Pregnancy, Schondinger Levi...) everything is dwarfed compared to the fucking literal end of the world.
The Genocide plot could work...in Context of being built up over the past 60-70 chapters. Also eliminate Paths, Ymir, Zeke sidling a bit, maybe as batshit as Eren but naturally a sociopath, to contrast Eren being a victim with his brother being a genuine evil piece of shit. You feel for Eren as people just manipulate him and he tries to resist, but his growing rage, schizophrenic identity crisis, the loss of friendship and isolation due to his superiors cutting him off from his emotional support. This leads him to basically embrace the Attack Titan's extreme emotional state of violence and bloodshed, because that's literally the only thing he has left. Make Eren a tragic figure, driven to madness by the exploitation of his own good will, the callousness of others and a monster his father made him.
I mean, that's a real tragic story. Eren comitting genocide not because he believes it, but because he has genuinely lost every single thing in his life and he is unable to bear the pain and rage of the Attack Titan's assault on his psyche no more. He no longer has any human connections because they were cruelly taken from him by the powers-that-be who viewed him as a perfect tool and not a person. The consequences come when they push Eren too far, when he has nothing left.
You could also make it so instead of Genocide, he seeks to stamp out all life in his madness, because humanity has been the source of his pain. Maybe through his former friends and allies, they bring him down and cut him out. With total devastation, there's nothing and no rules left to bind him. You've got a decision to free him from his madness or have him be so far gone he begs to die. Maybe there's a way to cut out the Attack Titan out of his body, or an ancient technology that is part of a McGuffin part. The final shot is a devastated world, but all factions have essentially been destroyed. There's no more Marley, no More Paradis, no More Eldians and no more Titans (ala the MacGuffin). The final shot is a crippled Eren, physically and psychologically, recovering with Historia, his child and Mikasa (ship Mikasa x Armin or something, this manga needs more emotion). The world is being rebuilt, and nobody knows if it will be as terrible as the old one, but leave them with a bit of hope, that the world is now free. Or do this with Eren dying, but I'm not a fan of throwing characters through extreme pain for a long time and just having them dying.
Of course, for my plot to work you'd have to DRASTICALLY change after the basement and limit KoM, Paths and Zeke. But that's really par for the course with 90% of the revisions that have to be done.
The sad thing is there's a LOT of interesting ways you can play this. And he basically chose the shittiest route.
Turns out Eren is Satan incarnate, wipes out all life and was just playing at that whole freedom thing and rules a dead land for all eternity while sitting on a throne of Marelyan skulls dripping with blood.