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>Team Rocket
Despite having unique character designs now, they did not stand out much from the original. Because Johto's plot is about Team Rocket being a fractured mess, they can't quite be taken seriously either way. I almost prefer them just being elite mooks in GSC, weird opinion I guess.
>Team Plasma
I don't remember much about the Sages from BW, but I like how they show up in 2 to repent and return the missing Pokemon. If you talk to NPCs in Driftveil City (where they now run some kind of shelter), people don't trust them and it makes them uncomfortable. It was nice to see this dynamic of change, and how there were characters in Team Plasma who weren't completely full of it afterall.
>Team Flare
Between the sci-fi inspired designs and their total lack of empathy, they feel almost inhuman. They talk very callously about necessary evils, how the Kalos wars were a good thing, or how they need to preserve their own instead of continuing to service the people. It's disturbing and their music compliments that feeling well. I think they might fit best in a different type of futuristic setting, though.
I have not much to say about Gen 3 or 4.
