Eh, Idunno.
I do see your point about playing as a villain or at least not as a stereotypical good guy, but I don't think Team Rocket's the best choice for that. They're just thugs who steal Pokemon, simple as that. No redeeming qualities whatsoever. Even the other teams are pretty questionable, Aqua's and Magma's end goals are really not all that well thought-out when it gets right down to it, and the Galactic grunts don't really know why they're doing what they're doing until Cyrus is gone.
No, I'd like to play as a Team Plasma member. At least those guys have a halfway reasonable end goal, and they have real conviction for their goals. The grunts really do believe they're in the right. It's more morally ambiguous than the simple "We're gonna steal Pokemon because we're evil!" that Rocket has.
Also, if I get to play when Plasma has that schism then I can go over to Neo Plasma and get that *****in' outfit.