I went back and watched Jones' snaps against Baltimore. Perhaps because the team was playing from behind, I wasn't appreciating what he was doing. He had some elite-level plays in the 1st half. Unfortunately he wasn't consistent and demonstrated some of the problematic traits we've seen too often in the 2nd half.
I really get the sense it's mental with Jones. When he's relaxed, calm, and in rhythm, he can throw the ball exceptionally well and be on-par with the best passers in the league, especially throwing the ball downfield. You could see a sort of hybrid between Brees/Peyton (I know people compare Jones to Brady a lot but I don't see it).
When Jones gets thrown off, faces some adversity, gets disrupted, that's when the bad habits come out: skittish in the pocket, dropping his eyes, bad timing/mechanics, throwing off the back foot, missing underneath defenders, poor decision making. Speculating here, but I expect Jones is probably better at practice than during live games right now, because he can be completely at ease during practice without the pressure of a live game. I sorta get the sense he has flashed more potential behind closed doors than we've seen in live games.
Combine Jones' upside/potential, along with his obvious conscientiousness, I can understand why the team would give him the opportunity to continue to start. I do believe, though, if you asked BB after giving a truth serum, he'd say Zappe has played better in games and led to winning football. But, the given the aforementioned circumstances - along with the fact Jones is still a 2nd year player - means it makes sense to continue to give Jones the opportunity to play and see if he can figure it out.
That said, 4-5 weeks ago the team likely believed they would have real trouble winning many games without Jones under center. Now they have confidence that the guy behind Jones not only will not lose them games, but can win them in his own right. If Jones continues to turn the ball (his most direct contribution to the losses), he won't start for much longer. While I believe BB is in this for the long-haul (another 4-6 seasons), make no mistake that he wants to catch Shula and he needs to start wracking them up now; if he feels Jones is losing them games, he won't play him much longer.
Will Jones figure it out? I don't know. When it comes to mental stuff, self-assuredness, ability to focus and sharpen during times of adversity, it seems some guys have it and others don't ... but it's not fair to write him off at this point. To my eye, Zappe doesn't appear to have the same issues with consistency (mental or otherwise); he's looked tremendously steady from snap-to-snap, and remarkably mature in every sense.
Hopefully this is a win-win for the team. If you get maximum potential Jones, the offense could be explosive and very productive - high ceiling. If you get inconsistent, turnover-prone Jones, you have Zappe ready to step in and lead the team forward with confidence.