The most likely characters who have a chance of disappearing are: Lucario, Wolf, Ike, Link Cartoon, Pokemon Trainer.
The ones who CAN disappear, even if it seems unlikely: Jigglypuff, Ganondorf (keep Ghirahim's arrival in mind, even if I'd prefer him to be a boss in the story mode), Snake and Sonic, Sheik.
Nintendo won't take the others out of the cast, I'm 95% sure of it.
The characters mentioned up above don't really matter to me, except Ganon, Sheik and Ike. And I totally support your ranting about Ike, Anacybele.