So does Camilla just run away from the kingdom? If so, that seems awfully out of character for her and if not, then Garon would find her one way or another and punish her for being unable to stop you.

I feel like what happened in the game made plenty of sense. Corrin may have many traits that are commonly found in shounen-like heroes, he's not exactly the most hot-blooded, especially in Conquest with its faint stockholm syndrome-ish atmosphere. I do think that it was a little too passive for my tastes (I'd rather he took a more aggressive stance before being physically held back and chastised by both Camilla and Azura) but it does make sense and to me, confronting Hans would've been the stupider decision and Azura and Camilla would've stopped him, telling him that it's not worth it. The whole scene is supposed to show Corrin the darker side of war and how powerless the siblings have always been.

I think you have to re-consider how much Corrin will defect from the kingdom because depending on his stance the amount of resources and allies available to him will be very different. I feel like he'd be extremely limited in your scenario and with the game revolving around bonds and connections, you can't half-ass and straddle the line in-between that Revelation and Birthright have set, not to mention the complications that would arise with the ongoing Nohr vs Hoshido powerplay. Corrin's siblings are absent for a good portion of the game because of the missions assigned to them, and they only join once they're completed to a satisfactory degree. The sibling feuds in your scenario would make Nohr a huge sitting duck. Basically, I think you're oversimplifying the war a little and need to make things messier (a country trying to revolutionize from the inside would have to handle forces from the outside and inside at the same time, meaning the player would have to alternate between repelling the Hoshidan forces and making their way toward Garon's throne), and the way Corrin defects should be different from how he does it in Birthright and Revelation. Also, though I said Corrin would be extremely limited, I don't think that's necessarily a bad thing. With proper guerrilla warfare and rallying, he can force opponents into extremely tight situations, and that might make for some very interesting gameplay mechanics and objectives. Just something to think about.

I like how you end Act 1 with the siblings reuniting properly, giving a fresh breath of air for the audience and the fact that you do not end the story with Garon's death, since (I assume this is how you want to make your script different from the original) Conquest should be about rebuilding Nohr. Ironically, I find that Birthright is more about conquest than Conquest itself and I think this would be a good way to play with the themes. However, Ryoma wouldn't be taken over by Anankos because of how different he is from Takumi- he's extremely confident and a very talented and capable person, unlike Takumi who has a huge inferiority complex, which is why he gets possessed/mind-controlled to begin with. Also, I think having Hoshido be driven by some supernatural force would be a bit of a cop-out and wouldn't be very interesting and Garon's death would mark the beginning of a new era, and Hoshido would likely become more open for negotiations. The conflict between Nohr and Hoshido should die out quite a bit and though there may be tensions and skirmishes, they shouldn't be the big bad from that point on, possessed or not. But then what? Who's going to be the bad guy? Anankos himself? That'd be stepping on Revelation territory.... I'd have Anankos!Takumi trying to incite another war between Nohr and Hoshido. Corrin and his gang tries to calm everyone and defeat the ones responsible, while tensions would arise between Nohr and Hoshido again. There needs to be more human drama than just swarms of invisible soldiers to put closure on the story.

I really like where you're trying to take this, but there are inconsistencies here and there. I know Conquest gets a lot of flak but at the very least, the plot still drives through a well-made road. It takes conflict and themes that differ from Birthright and Revelation and places them at the right places (though that doesn't necessarily make it an amazing story). I dunno, but that's how I feel. Anyways, I hope I didn't sound like an ass, I just get really excited about this kind of stuff and love talking about it.