The problem could be a little bit Ken Dorsey. I've read that we have a deep to shallow passing progression, where Allen is supposed to look deep, then intermediate, then short for a dump off. If the deep stuff is never going to be there, then this offensive philosophy is flawed and will have Allen standing in the pocket too long.
I think we're going to need more than 1 game against an elite defense (probably top 3 with the Cowboys and 49ers) to know for sure. By the midway point of the season we'll see if the TEs are actually getting more involved.