From what I have seen so far in SSE, it seems that there are the main villains, such as Wario, and Boswer, and the big bosses. The villains use the trophy guns, track down the heroes, etc. The big bosses do all the dirty work, Petey was to capture the princesses, Rayquaza was to destroy Fox's ship.(I think that when the Halberd shot down Fox's Arwing, that the SSE sent Rayquaza to finish the job. Hence why he shot st the Arwing when Diddy found him.) The villains are PCs and are character size, when compared to the bosses. The bosses are huge, and cant be fitted into a playable character, so instead of ATing them, they give them a role in SSE.
My list for Villains: Boswer, Wario, Ridley,Dark Samus, Star Wolf, King Dedede, Ganondorf, Mewtwo, Giovanni, and some more
My list for Bosses:
Petey Pirhana, Chain Chomp, Andross, Kraid, Mother Brain, Any of the big Legendary Pokemon, Kracko, Whispy Woods, Ghoma, Ganon(Beast form), and others.