I agree with that. I don't like being in the shotgun on a short yardage down and in a short yardage situation. The whole point with the shotgun to start with is to give your QB a head start on the pass rush and to the defense better.
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I don't mind a guy like Dak doing it from the shotgun (mm hmm). He's able to get a head of steam and move anyone who may hit him forward a yard or two. If he's under center, it's tougher for him to be able to move anybody. You just have to rely on your OL then to get the push, and if they get the push you need from under center, it should be enough for you to convert from the shotgun, too.
If the DL is hitting your QB in the backfield in a shotgun set, you weren't going to convert it from under center anyway.
What I hate is the lack of creativity of any kind. I would run some speed option here and there, have him throw it every once in a while...