Starkiller in The Force Unleashed II is in fact the real Starkiller, just with a bad case of amnesia. All the other clones of him are failed mutants, and other cloned Force-users in the EU were mad (Luuke for example), or had to transfer essence or whatnot. Besides, thematically I think it works better with Starkiller’s story about identity and I do believe it would have been revealed in the third game.
Yoda is from Kashyyyk. I came up with this when I was younger to explain Yoda’s good relationship with the Wookiees in Revenge of the Sith. I know The Clone Wars was going to give a reason for it in an unproduced arc, but I think its possible it could have worked out still. (Not that it needed an explanation of any kind, nor is my theory the only possibility of course, I just like clinging to the idea since I’ve had it for so long.)
The Academy Luke references in A New Hope and its deleted scenes was not the Imperial Academy, but rather just the Star Academy. Luke was either referring to the Academy founded on Tatooine, or one that was more of a galaxy-spanning institution. The Imperial Navy was known to sift through these Academies for promising students to lessen the amount they needed to train themselves.