Oh absolutely, JP and RJ had bad habits. I think just about every QB going from college to the NFL has some. I would guess that the FO has to weigh the good against the bad habits, assess if they think the bad habits can be corrected (or not), if the bad habits are going to be show stoppers for their particular offense, probably a hundred other decisions, and then make a decision. The current career status of RJ and JP would seem to indicate that they were not good choices by the Bills FO. And I'm not passing judgement on the Bills FO. There have been enough Ryan Leafs, JaMarcus Russels, David Klinglers and so on to share among GM's. As well as Brad's, Manning's, Brees' and Favre's.
I would imagine that teams want to develop a particular type of offense (for example) based on what the executives and coaching staff decide. And then they go out and try their best to acquire the personnel to achieve that end. In the Bills case, for whatever reason(s) they decided to stick largely with the current group of offensive players. So it would seem their philosophy is to develop the offense around the players they have rather than develop a particular offense per se. Luckily, that seems to be one of Gailey's strengths. As trite as this sounds, the outcome of any decision is: things get better, worse or stay the same. We're going to have to see how this one plays out.