In this thread, you can basically just post what they're teams would be, where they would be, and how you would get to them.
I'll post one to get it started.
Drifblim (was found in the Valley Windworks)
Blissey (Happiny Egg was given in Hearthome City)
Lucario (Riolu Egg in Iron Island from Riley)
Porygon-Z (Porygon from Veilstone City)
Togekiss (Togepi Egg in Eterna City from Cynthia)
You obviously don't have to make your team like mine at all, I'm just posting an example.
and yes. You can change Red's Team.