The White Suit: I think it's just asthetic. The suit is for show. It was something worn often by Tron in the old days, so it's recognizable. Thus, when Beck or SPOILER... Mouse Over To Read:
wears the suit that was basically Tron's signature, they are instantly recognized as Tron. As for the inconsistency, look at it this way: we know Tron was taken and injured in the coup while defending Flynn and giving him time to get away. That's the important part. Whether his suit was white or black is merely design choices. It could hav happened either way. In one regard, the flashbacks we have in Legacy are faulty because Flynn's memories of the event are fuzzy. We only see it from his point of view. In another, Tron's memories could be faulty because of his damage. We only see it in Uprising from HIS point of view.
I think that the white suit issue isn't a big deal. It's to emphasize that he's TRON. The above is my attempt at reconciling it in-universe.