Personally I believe Russ is the better QB and we'll see that this year. If you look at the stats (I know, I know) Kaepernick is only a few % points behind Russ in accuracy, and he's ahead of him in YPA. So, he hucks the ball a ways downfield, but is still accurate. Add to it that he has a damn good work ethic, seems to have decent intangibles, and his physical stature, plus he really does impact games to a large extent, and he's the real deal.
It's like Dilfer said one time, Wilson isn't doomed because he's short, but you have to be exceptional in every other part of your game, which Russ is. The flip side of that coin is that when you're built like Kaepernic and Newton, you have more margin for error. You see the field easier when you're 6'5" and don't need to rely on throwing lanes quite as much. Add to that the athleticism, and the fact that Kap doesn't look to run first, but scrambles to throw, then runs (kinda like our guy, but to a lesser extent) and he's a big weapon.
Throw in the fact that he has a better QB guru coaching him up in Harbaugh and it's no wonder SF fans are giddy.
SF has also been a relevant franchise a lot longer than we have, it's no wonder that Kap's jersey sales are higher than Wilson's. It's actually surprising that Wilson is 2nd on that list, and probably a testament to the solidarity of the 12th man and maybe evidence to our fan base growing.
