Oh, and also, you gotta make the whole PATHS shit way more ambiguous and unreliable. Make it so that EREN thinks genocide is the only option and won’t hear otherwise, but it should be clear to the OTHER characters (and the audience) that there’s other solutions to be had. You also don’t make the rest of the world strawman racists - maybe Eren thinks they are because that’s how the previous Attack Titan users saw them, and that’s seriously clouding his judgment, but it should be clear to everyone else that he’s wrong.
I mean, there's also the option that Eren is right. Just not in the way people were expecting.
Make Eren the equivalent to Cassandra. Have him figure out that the world developed an equivalent to a nuke, but nobody believes him. Have him explore every avenue to try and avoid killing the rest of the world. The world itself basically decides that Paradis is more trouble than its worth and decides to off it. Show that the world is only tenuously united through its hatred of Paradis, and machinations behind the scenes look to rid itself of the excuse. Maybe you know, make another antagonist. One who is hyping up the use of the only nuke on Paradis to rid themselves of the devils, but his nation already has multiple ones ready to go to dominate the rest of the world, once they nuke Paradis into oblivion.
The problem is that every avenue Eren explores leads to the destruction of Paradis. Not only that, once Paradis is destroyed, humanity destroys itself through nuclear annihilation. It doesn't matter if Paradis and the Eldians are euthanized and killed slow or fast, humanity is destroyed in a massive world war followed by waves of nuclear fire. Every single avenue Eren explores leads to this conclusion. The annihilation of Paradis, followed by the annihilation of humanity itself.
Nobody believes Eren because nobody wants to believe him. They all think he's lying or gone insane. Nobody tries to help him. He tries to do everything himself. Maybe the only one who believes and helps him is Historia, but for the reasons in the plot she can't do it actively and has to hide. Eventually, he just cannot hold back anymore and the march of time eventually forces his hand.
He has no other choice but to annihilate the nations of the world, taking the secrets of the nuke (or whatever weapon you want) with them. They're all too close to completion, nobody is willing to help him and he sees no other alternative. He can't just destroy the weapons, because every road leads to destruction. The only road he sees to humanity's salvation is the destruction of the civilization on the mainland. There's simply no other way, the hatred of Paradis blinds the world to its own destruction. Any half measures Eren takes inevitably ends up with humanity's demise down the line.
So Eren's only way is through the rumbling. Of course his friends constantly try to stop him, and he avoids killing them, but they refuse to believe him and he has to kill them. So they force his hand. Eren ends up destroying all of humanity on the continent, along with all of the super weapons he finds, and the evidence to their existence. Only he and Historia knows about them. With the destruction of the mainland and all the shifters, all of the Titans go back to Eren, who finds himself basically immortal as the last Titan, with the memories of all the shifters inside of him. Unable to cope with what he's done, he despairs, and now something beyond human itself, he decides to leave the world behind.
Eren himself decides to disappear into PATHS, sitting at the end of time and space itself. He stares at the Yggdrasil, wondering if he made the right decision to spare humanity a species bent on its own destruction, now being something other than human himself. When he sees Historia and his child in the world through time, he decides that maybe, just maybe, there is a faint hope with everything he did and sacrificed, perhaps humanity was worth saving in the end.
That's most likely what was going to happen originally, Linked Horizon would get insider info from Isayama and put bits of foreshadowing into his cover art and videos. The most explicit being this:
Though the difference being this Eren has a kid and the kid keeps him from killing himself out of guilt. Yes he's a fucking bird here too.
Wow, that brings back memories. Turns out that video was completely fucking irrelevant lol.
