I don't see where JVB's problems this season have anything at all to do with the system he's running.
Just look at the types of problems he has....completely missing wide open receivers, failing to go through progressions, poor footwork resulting in inaccurate throws, panicking at the slightest sign of pressure and dumping off to the outlet guy who has no chance to make a positive play.
The fact of the matter is, despite what appeared to be a lot of promise as a freshman, JVB just isn't a very good QB. I have no doubt that he works hard and is a good guy, but he really should have been benched a while ago in favor of giving one of the younger guys a chance to gain some experience for next year.
Kirk has a stubborn tendency to maintain continuity at all costs. In previous seasons he was able to use that to his advantage when his teams steadily improved throughout the season and wound up pretty good at by the end of the year, when things may have looked bleak early on. But during a season like this, it only makes him look stodgy and foolish.