I think the weird thing about Aqua is that the fact that she doesn't play any part in the villains' plans is what makes her so effective.
Ven is trapped by Master Xehanort's plan to turn him into the χ-blade, and is never really able to subvert that.
Terra is trapped by Master Xehanort's plan to use the darkness inside of him to turn his body into a vessel for Xehanort's heart, and he's never really able to subvert that either.
Aqua's the only one who's able to throw Master Xehanort's calculations off, because she doesn't really figure into them. His only use for her is to stuff her in the fridge to draw Terra and Ven even closer to their fates... except that Aqua's not having any of that, survives all attempts on her life, and then proceeds to use her wildcard status to mess up everything he worked for.
...but, for that to work, it means she can't be given a consistently-antagonistic figure of her own, which makes her seem less relevant early on. =/