I know last offseason he spent a lot of time working on getting back from center quicker so he'd have more time to go through his reads. He also wanted to work on not sliding forward in the pocket and creating pressure that wasn't there.
From what I understand this offseason and in the pro bowl last year he wanted to work on throwing vertical routes up the seams. I'd expect to see him and Witten working that area early and often this year.
Personally I'd hope he's working on his deep ball. I know people question his arm strength, and even though the deep out is the true litmus test for arm strength - I'd like to see him air it out a lot more this year. In one on one opportunities give guys like Miles, Dez, and Roy an opportunity to use their body and leaping ability to go make plays. He seemed to have good chemistry with Owens on the deep ball during their time here. More often than not when you take shots you either get a big gain or a PI penalty called.
He doesn't need to throw it up in double coverage - he gets berated for not taking care of the football enough, just give his receivers more chances to make plays on the football.
Just my thoughts.