Magma and Aqua held a better storyline with Groudon and Kyogre. I also loved how they each thought they were doing a good thing to help Pokemon, giving more place for them to live, not thinking they were doing anything bad.
Team Rocket would've probably been the same old thing, wanting to capture the weather trio to control the world. But anyways, Team Rocket's region is Kanto & Johto, what the hell would they be doing in Hoenn anyways? It's not their turf.