Definitely agreeing that they're more "bad" in Unova, in that they*'re actually doing some bad stuff, instead of just irritating Ash & co. every episode. And they seem to have more of a "plan". It's actually quite nice to see them getting some sort of "in depth" storyline. I'm currently watching Master Quest as well as keeping up with Rival Destinies, and they are SO much more irritating in the older seasons with their incessant attempts at stealing Pikachu.
*When I say "they", I mean Jessie and James. I think Team Rocket as a whole always had "bad" going on, but you never really see too much of other TR members.