Because Pryor is still young and inexperienced, he is prone to rookie mistakes.
The best example is in the picture for this slide when he slid down in bounds just before halftime in San Diego. With no timeouts left the clock expired, and sure enough the Raiders lost by a field goal.
Even if David Akers was the kicker, Pryor needed to get out of bounds so the Raiders could try to get three points. Especially when Sebastian Janikowski is your kicker, a few yards aren't going to make a difference for him.
Pryor also appears to be lacking in the arm-strength department, as many of his passes seemed like a lob that you would see in a game of three flies up. He needs to add some zip to his passes. While he had just one interception against the Chargers, if he were playing a better defense he would have had some interceptions with some of those lobs he threw.
With Greg Olson as the new offensive coordinator, Pryor will need to work on his arm strength for those deep passes.
Another knock on Pryor is his chemistry with the receivers. Palmer simply has Pryor beat just because of how much more playing time Palmer has over Pryor.
Pryor may be the future for the Oakland Raiders, but that future is still a year or so ahead.