I think that's where my main gripe with 3 lies because it's the start of the complete malarky of Gen 4.
In 1 and 2, there was a story, a bit dark and sinister at times. Evil organization in a Casino and puppeting a shell corporation, cutting off Slowpoke tails, graveyard, what have you. And when the story didn't explore these tangents to an otherwise perfect world, it would use the legendaries and focus on a creation story.
Then Gen 3 came along, and split Rocket into Team Magma and Aqua, which is just bloody lame. No way around it, that's just stupid. Furthermore, it told the creation story again, only now segmenting it even further among legendaries that are even MORE mediocre than regular Pokemon (save for Kyogre, whom is actually quite the statistical beast). On top of that, there were some fine designs (Tropius) mixed in with some god-awful scribbles.
And then, what I feared would happen, did. Gen 4 went down the DARKNESS AND EMOTIONS path that has been the demise of Megaman Battle Network, Megaman Starforce, and Kingdom Hearts. To add further injury to the creation story, now you've introduced beings that control TIME, SPACE/MATTER, what essentially is the GOD of Pokemon, and yet they can all have their asses handed to them. Worse, the designs throughout this game were infinitely worse. Whatever gameplay improvements there were are far overshadowed by the sheer ruination wrought by the story.
Here's hoping Gen 5 kinda gives the series a clean slate.