I'm hoping that Team Aqua get some more Pokémon! Don't get me wrong, I do love the four families they use now, but I really think they could've picked some stronger Pokémon to use. Introduce things like Wailord, Octillery, Wishcash, Kingdra, Lanturn, Kingler, etc, basically any Water types, and they'll be much stronger. I think that partly the reason they have the Pokémon that they do now is that those Pokémon are supposed to resemble evil, but I don't think this is the image that Aqua/Magma should have. They aren't evil; they're doing what they're doing because they think it'll improve the world. They're actively trying to help people rather than hinder them, so I don't understand why they only use evil-associated Pokémon. With teams like the Rockets, it's obvious that they should be using these Pokémon because they're trying to take over the world, not improve it. But I don't think Aqua/Magma should appear as evil like that.
I'd also love to see the leaders catch Kyogre/Groudon and fight with them; that'd be amazing to watch.