Is it okay if I define "theme" as something that's shared by more than half of the team, or shared by the highest level Pokemon and at least half of the team, and ignore teams that have only one species?
If this definition is good, then I think these are all the "theme" teams in Colosseum.
Miror B: water, grass, special defense (his team is 80% Ludicolo, and his other Pokemon doesn't fit any of these "themes")
Skrub: physical defense
Dakim: ground
Ein: speed
Gonzap: physical attack
Evice: physical attack
Gonzap: physical attack
Miror B: water, grass, special defense
Agnol: physical defense
Resix: fire, special attack
Blusix: water
Yellosix: electric, special attack
Purpsix: poison, HP
Greesix: grass, physical defense
Naps: physical defense
Lovrina: speed