I honestly don't think Xehanort's eyes were always yellow. I mean, what is he then, an alien? Vanitas was apprenticed to Master Xehanort but was he meant as a vessel? Let's not forget he had yellow eyes too.

My big issue still is whose Nobody is Twilight Thorn?
BTWFYI, I think Axel's Heartless was Trick Master from Wonderland.