Seriously, like that will ever happen. The closest it ever came to that was when Giovanni tried to find Mewtwo in 'Mewtwo Returns.' I'm afraid the anime is far too childish to come up with something like that. They focus on morals such as self sacrifice and hope and love and everything people hate to see in a film. That's why kids love it and adults don't.
I'm planning on making Team Rocket integral to the third sequel of my fanfic, with the main characters having personal hate for the organisation and their leader and thus giving them a motive to take them on.
Its a shame, really, that the anime never have done this in the past. They could have been so much more successful with the older generation as well as the younger ones; just keep Pikachu for the younger generation and it would have all been fine.
Nice idea, but it's unlikely it'll ever happen in the way that you and I enisage it.
"Play with fire and expect to be burned."