I'd probably lead up a vigilante group that shows up to places just to trounce team rocket. So... I guess what I'm saying is I'd be the Batman of the Pokemon world and there'd be some other guys to be the equivalent of the lame superheroes that make up the Justice League core.
Either that, or I'd be a part of team rocket. Taking what I want, but enforcing my own methods and rules. Hmm... =/
Barring those... probably a poke-cop. Something to do with semi-frequent battles, challenges, and travelling.
Any which way, I'd use my favorites and cultivate their potential. (Also, no 4 move limit as in the game.) So, I'd have blastoise, torkoal, gengar, and others. With a psychic type- Mewtwo or Alakazam- to telepathically relay my strategies, thoughts, and emotions to my team. Cuz hey, it's kind of a disadvantage if your screaming out attacks lets your opponent anticipate them and perhaps counter them. Plus, it's not like pokemon would actually have to be ordered to attack to use one. So with their connection to me, they see what i envision, and perhaps be inspired to come up with new techniques on their own.