You do know that the claim that JP doesn't throw short accuratly is a myth, right? JPs completion percentage on short passes (and long for that matter) was better than that of Trent's last year. Those numbers (broken down by yardage) have been posted on this board more than once. Also JP was more accurate this past pre-season and also this year in the time he has played. So for Trent's career in Buffalo, JP has a higher completion percentage both short and overall. That is a fact. I don't have time to dig for last year's numbers but if you look, that is exactly what you'll find with absolute certainty.
As for the rest of your "proven facts". We really don't know the coaches reasons for making the change and probably never will. This is not to say that Trent won't be a very good starter. We've seen evidence of that. JP with a fresh start may be as well as you pointed out.