This a room for non-competitive ideas/suggestions.

[Lord Windos]

So this is just a random idea, but put Professor Larkspur back in the game. He's the closest thing to a villain this game has and there is a lot you could do with him. For instance, maybe he tries to control Aotius and Mutios with SCIENCE and causes the player to fight them in a double battle? Or, perhaps more basic, he figures out how to reveert Urayne back into Gamma Forme and tries to rule the world like that, and at the end of the event you could recieve something like the Blue Orb in ORAS that transforms Urayne into gamma forme during battle.

Also, destiny knot in the game for breeding purposes. Those of us who missed the event are mad because of it.

Not trying to spoil anything, but there is a bigger and more important villain later in the game.

... Eh? If you're referring to the endgame villain, that person gets off due to the circunstances surrounding that person. Not really a "true" villain IMO, unlike Larkspur who does it for teh evuls.

'They' are still a Villain, despite the circumstance surrounding them, as up until you are told all the details, it seems they are a deranged maniac bent on bringing a Nuclear Apocalypse. Having more Villains in the story would be nice, though.

Hehe. (CAUTION, MAY CONTAIN SPOILERS!) Looks like I am the only one who is on her side... despite everything. She had her reasons, or rather I can understand why she probably pullled it through once started. It's not like she could stopp it all at a desired point, Urayne played a huge role in this. Plus her scientific mindset that started to run for itself.
At least, I don't really see her actions as "crimes", but rather born out of tragic occurrences and a brilliance that was a bit too close to the maniac side.  (POSSIBLE SPOILERS END HERE)

Well, that's my point of view, and you can agree or not. But I don't want to argue, I can see your points, it's just... well, I dunno. Either I'm totally mad, but for my defence let me say that I rather think for myself than to follow the opinion of the mainstream, or I simply read too much in a game.

*gets ready for approaching haters*

Its not like I can't understand that point of view; heck, I prefer it, rather than the dreary story of 'Yeap, they're pure evil, send them away.' It is a tragedy that happened to them, but the thing that makes them shade my opinion negatively is not their actions, per say, following their 'birth'. Its what they'd risked and sacrificed in the process: family. If it was not for that, I would be completely on board with the 'They did no wrong, its just science!' argument.' As its stand, I think of them as a tragic figure that got completely over their head, one way or the other, and ended up paying for it with their sanity. Yikes, now that I said that, I feel even worse about their crisis. Thanks me......