Could be intelligence, could also be experience if he's less experienced than your other QB. Also look at field of view, that influences the QB's ability to locate another receiver that's more open than his primary target as well as to see the defense.

As for intelligence, the dumbest plays better, and his field of vision is worse. Experience is the same.
What i like about it, is that my qb doesn't play like last year. I find it headscratching, but i love the idea.

A new game engine version (0.3.1) replaced the old one with new seasons (If I understood things correctly)

Ah, yes, this is true - the QB is now more susceptible to the pass rush, the OL/DL is more important to your QB's performance than before.