This a room for non-competitive ideas/suggestions.

[Cataclyptic]

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.