I think the challenge is that Hilinski is pretty good.. when he has a pocket and he has time. In camp due to hitting restrictions that is available. Against Nebraska with a weak pass rush he was good. Then as the season wore on it got worse and worse. I obviously wasn't at the fall camp practices, but it's entirely plausible that Hilinski looked like the better option there, but turned out to be a suboptimal play as the actual season progressed with a bad OL leading to worse play and loss of confidence.
Would think Fitz and Bajakian take that experience into account as they are making evaluations this year... I have no view on who should start, but it should absolutely be an open competition and may the best man win.