I do like Derek Carr's upside more than Kaepernicks. Kaepernick is coming up on 3 years as the signal caller of the 49ers and he hasn't made any significant progress. He looks exactly like the guy he was 3 years ago when he first took the reigns. Kaepernick is a decent QB that will take care of the ball, and make big plays every now and again, the problem is he will never be more than that.
He still has a slow, funky weird release, he still has not learned how to put touch on the ball, he still has not learned how to look off his receivers, he progresses through his reads rather slowly, and his pocket presence can be very erratic, and his accuracy is hit and miss. None of these flaws have really been fixed, or really improved upon.
Carr on the other hand looks like he has a very bright future. This is a case of potential vs. a known quantity. Carr has been dealt a crap hand in Oakland, yet is thriving in such a poor environment. Sure his TD:INT ratio, and his Yards/average are not very high, but lets remember, he has the worst supporting cast in the NFL.
One thing I need to make mention of is Carr's lightning quick release. Unlike his brother he does not hold unto the ball for very long. At the end of his three step drop the ball is almost always out of his hands. His release speed, decisiveness and presence in the pocket are eye popping, especially coming from a rookie. I expect good things to come from Carr if he ever gets a decent supporting cast.