My guess (and it is only a guess) is that he is comfortable in the pocket for a shorter amount of time than a lot of QB's that can't quickly decide to make something happen with their legs. I imagine the mental factors can be quite tricky to deal with. When he decides to take off, obviously it's harder to keep track of receivers down the field, and when he's hanging in the pocket fighting off temptations to run, it might distract him from what the D line/LB's are doing.

Bottom line, and it's a dead horse being beat by now, his ability to escape the pocket has probably slowed his progression as a high quality pocket passer. That's not a knock on him, but just a common tradeoff with running QB's.