Hell yes I would. I've been wanting to play a Pokemon game where you played a villainous character for a long time. (You -could- count Colo since Wes was once part of Team Snagem, but he cut ties with them when he stole the Snag Machine, so.) As for team of choice, I'd pick either Team Rocket or Neo Team Plasma. I love Team Magma, but I'm not the biggest fan of their goal/how they execute it XD
Anyway, if I were a part of Team Rocket, the main thing I'd love to be able to steal/take Pokemon from Trainers during battle (could bring back the Snag Machine, haha) or after battle (could sort of be like that one tournament in YGO where you give up your strongest card upon losing). I'd also like to be able to steal items, namely key ones. I mean, you find potions and stuff lying around in the main games anyway; I doubt they'd take that aspect out XD It'd also be cool if Red and Leaf or Ethan and Lyra (or Gold and Kris for nostalgia) were your main opponents and are trying to stop you from completing Team Rocket's goal. Oh, and you'd have at least one "rival"--another Team Rocket member who's trying to be better than you and will battle you constantly. Instead of earning badges, you'd have missions--e.g., steal a rich person's Pokemon, capture a legendary, etc. After completing a certain number of missions, you'll receive a badge (stolen, of course), allowing you to use HMs. You'd also start as a Grunt, but the more missions you complete the higher you'll be able to rise in rank. There could be extra ranks rather than just Grunt/Admin/Scientist so you have more to look forward to.
If I were a part of Neo Team Plasma, I'd want the same as for Team Rocket except the Pokemon I steal I'd have to hand over to Ghetsis. And, of course, Nate, Rosa, and N would be your opponents. It'd be cool if Blair & Whitlea came back to stop you, too o:
In response to the last question, I'd probably join the good guys on some of my playthroughs. It'd be cool if you could then take on gyms (though it'd be optional) and the leaders' Pokemon would be at reasonable levels (e.g., if the Trainers' Pokemon were in their 40s by the time you switched sides, the first Gym Leader you challenge would have their Pokemon in their 40s or 50s).