Since we have only two choices, I go with Kapernick for two reasons. Firstly, I think he is a more intelligent runner with the ball. RG3 attracts trouble, hence his multiple knee surgeries. Kapernick's long ranging stride is decpetively fast and he is clever enough to minimise risk to himself and mature enought to slide when he has to.
Secondly, the knee injuries. I don't care how well RG3 is coming back from knee surgery. He's had far two many imo, especially for such a young age. It will take it's toll as time goes on. Kapernick has a clean bill of health with his knees and has a running style that involves a lot less risk. So he would be my franchise QB choice.
