[r3v3n63]

Since you picked the good guys I'll do the villains;
Micronauts: Baron Karza and one of his Acroyear lackeys
M.A.S.K: Miles Mayhem with Switchblade
Centurions: Doc Terror
Transformers: Rumble and Ravage
D&D: Warduke
Visionaries: Cravex
GI Joe: Cobra Commander and Destro. (I know they have been done to death but if they were re envisioned for this new universe they could really do something unique)
Something else that might be an interesting thing to include is Battle Beasts (which were a Japan Transformers spin off) They could mesh up with the Inhumanoids/Primordia angle.