I wondered as well why they added Yoda and Darth Maul because none of them had any real affiliation with the Rebel Alliance or the Galactic Empire at all.
It makes no sense that Maul fights for the empire because he had it in fact against him. Him being on the side of the empire only make sense if his plans to take Palpatine's place had succeeded. Well, on the other hand it doesn't make sense that Maul is fighting for the Separatists either...
Though we don't want to miss playing Darth Maul out, do we? Else we need an extra game that's focused around his arc on Naboo and Mandalore.
Same for Yoda.
Just consider it to be some kind of alternate history or own head-canon in regards of hero choices.
Not even mentioning that other heroes like Bossk didn't take part in any of the game's battles at all, at least according to screen sources.
