I forgot about the game guide. It's how I found out all of Melee's cast before even placing the game in my Gamecube disc tray.
You have kind of answered your own question. Pokemon trainer is the master, the commander, the owner. The character could be called Squirtle, Ivysaur, and Charizard, but that would be quite odd, don't you think? That would also imply that the pokeball from the 'pokemon change' move, came out from the sky or something. This is more unique, and better because I'd rather one character slot wasted than three. It's quite original.
I can't tell you anything about Shiek, yet.
Zero Suit Samus has everything that makes her her own character. Four B attacks, a Final Smash; the works. Notice how POKEMON TRAINER has one Final Smash? And not each of the Pokemon? I'm sure you will be able to play as Zero Suit Samus right from the begining (like Shiek), and I wouldn't doubt you would be able to cancel Samus loosing/gaining her suit durring her final smashes. That is just my opinion.