Lol I agree, anything made after Team Rocket just sounds lame. Now they've got Magma and Aqua, I think they're making a Team Galaxy...it just gets cheesy after a while. If they're going to do the same things as Team Rocket (steal pokemon, exploit trainers, etc) then I say keep Team Rocket. If they aren't, then change it, maybe think of one person who will be the sole leader and mastermind of the group and plan it around that character instead of picking a word to go behind "Team" and then limiting all of the members to that.
When I make up town names, I like to think of colors (since they do that in R/B/Y). If you can't think of an unusual ones, get out a good ol' box of Crayolas or go to Thesaurus.com and type in a regular color. Types of rocks make good ones too, like Garnet, Opal, Amethyst or Turquoise. Make sure you can provide a map if you do make up a new world though, otherwise it's too confusing to the RPers.
Also, make sure to give each town a personality. It'll be more interesting that way rather than just "Oh look, now were in Rock City. There's a lot of rocks..." Tell about what sort of people live there, the size, what the climate is and maybe any special geographical or cultural features. That will also give everyone an idea of what pokemon might be found there.
Good luck with your RP, hope you can take something from everyone's ideas and make something great out of it.