EJ had some decent moments in 2013, he has his flaws, no doubt, but I've always felt the tandem of Marrone and Hackett was a terrible combination for developing a young QB. Marrone preferred the inside zone runs and was not very flexible in what style of offense he wanted to run. I forget who said it but it was an OL during a minicamp in Rex's first year and he was asked the difference between the Marrone/Hackett offense and the Roman offense and the guy said all Marrone wanted to do was run inside zone whereas Roman was implementing the wide variety of blocking schemes he likes to use. And then of course, Marrone and Hackett are both first timers at their positions in the NFL. They have a QB who trusts himself the most to make a play which leads to him leaving the pocket early, dropping his eyes off his reads and taking off for a scramble. Normally, coaches want to teach a young QB that he's going to have to hang in the pocket and wait for the play to develop and not take off at the first sign of trouble. However, I remember quite distinctly that Marrone/Hackett both encouraged EJ to run whenever he felt like the play wasn't there. They preferred EJ take off and gain a few yards rather than throw an incompletion or an interception. As a young QB you've gotta let the guy take his lumps and learn from his mistakes. Given EJ's slower processing time and the fact that he didn't trust himself to fire the ball downfield into tight windows or throw receivers open, telling him to scramble rather than try to make the throw simply reinforced bad habits EJ already had.
In near-perfect situations EJ showed real NFL ability as a QB. And by near-perfect I mean a clean pocket, his footwork is in sync with the routes his receivers are running and the pocket holds up long enough for him to correctly apply his mechanics and accurately deliver the ball for a completion. Unfortunately, those types of situations don't happen very often during a game. QBs need to be able to work in a muddy pocket, avoid pressure, look off the safety, go through the reads, make a decision and throw all within about three seconds. After that, things start to fall apart and improvising comes into play, and EJ's improv was just to give up on the throw and take off.
You can see as he went from the system used in '13 and '14 to the ones used in '15 and '16 that he was trying to become more of a pocket passer without his first instinct being to run as soon as trouble arose. There's no doubt about his athletic ability and his work ethic, unfortunately for him, his biggest hurdle is the mental processing aspect and how quickly it needs to be done. Perhaps that's why Marrone/Hackett encouraged the running? Maybe they knew it was going to take the guy quite a while to adapt to the speed of the game so maybe they thought they were keeping it simple for him by giving him half-field reads with a near-constant option to run, I dunno. He's a good dude, it just hasn't happened for him. However, with Oakland's OL, I kind of expect him to beat out Cook for the backup job out there based on how good the protection is from the Oakland OL. Carr was sacked only 16 times last season. Granted, Carr makes his reads and decisions faster but the more time EJ has the better simply because he just doesn't process things as fast as needed in the NFL.