There are several reasons the coaches may think the shotgun is not the best for this team right now.
One reason is for the elusive nature of Ball. Under center, outside blitzers run to the QB - Ball has shown time and time again the ability to roll out and outrun even F$U speed to the corner. In the shotgun, you take much of this away, as the blitzers run to the shotgun position, forcing the QB back into the pocket (where Ball has had almost all of his sacks), rolling out from the shotgun puts you about 10-15 yds behind the line of scrimmage.
Remember, we were in the shotgun quite a bit last year with AJ - the shotgun actually benefited him from a speed perspective, because he was not going to outrun anyone to the corner. If you recall earlier in the season, when we were trying more play-action with AJ (ala the clemson game), he was getting eaten alive with the outside blitz.
Also another reason the coaches may not feel they want to utilize the shotgun package is that it eliminates the play-action fake. This has been a pretty powerful tool for us, even in the limited amount of scoring we have had. If you recall, the TD against AU was a result of play-action - of course we had some success running the ball out of the backfiled, which is requisite for the play-action to work, but on that play, the FS was clearly frozen for a second while Logan ran a flag pattern out of the slot.
Also our backs have not been the best at picking up the blitz lately, again limiting the desire for shotgun - if you are in shotgun, you are almost assuredly going to get blitzed, as the worry about the run via dive play etc is not as severe.
Also, if you talk to ex-QBs, they will tell you that you actually have *less* time to read a defense out of the shotgun - you have to concentrate on the snap, and lose about half a second of reading what the defense is adjusting to at the snap of the ball. Under center a QB can watch the play develop as he breaks into his back pedal.
Overall, the shotgun is great to give more time for a less-than-mobile QB who excells at reading defenses. If you recall, we were in shotgun a ton with Godsey in passing situations (I think that QB description fits him to a tee), but we really seldom ran Joe Hamilton out of the gun.