Thompson is the better athlete, but shorter, not as good of a passer, but a gamer. Has grit. Major accuracy issues though.
Wilson is the better pocket QB, but he does have some mobility. But he does tend to turn it over more, mostly because he takes risks. Makes a lot of plays taking risks though. When healthy, probably the better QB with a higher upside.
What could possibly go wrong for the U this year with 2 guys wanting to play QB, and neither seeming to have won over the staff/team yet?