I agree Smith got a raw deal. I like Smith still and everything I hear about him is that he is a stand up guy. Everything I hear about Kaepernick is the same though, and Kaepernick is still very young. Whether or not he'll mature into a great QB or not remains to be seen, but it is far, far too early to write him off. Look at Smith's first seasons. Yes, Kaepernick's performance in the second half was dismal, something he wouldn't contest, but to pretend he is throwing interceptions left and right ignores the statistics. In the end he'll get better. How much remains to be seen.
Kaepernick stepped into the starting role on a team poised to make a playoff run, so I don't think it's fair to compare his early career stats with Alex Smith. CK's stats aren't bad at all, but from what I've seen, he's getting by on arm strength, mobility, and the talent of his targets (two top tier WR's + Vernon Davis helps a lot, imo) and not from making the right decisions at the right time. That's why I think he's got some Favre in him. He's going to make some great throws with that arm, but as he gets older, more and more of them will get picked if he stays as dumb as Favre did.

As to Romo, minding that as a Niners fan I dislike the Cowboys, he gets a really raw deal from the fans. The Cowboy's offense puts up 48 points and loses the game 51 to 48 after Tony Romo throws a late game pick and fans blame Romo for the loss. I have news for them, if your offense puts up 48 points and you still lose the problem is not your offense. The problem is that your defense's complete inability to stop the other team keeps putting your offense and QB in a position where they have to come up with late game heroics to win the game. Late game heroics are always more likely to burn you than a slow, persistent and controlled drive.
I'm a Cowboys fan. That's hard for me to type these days.

Yes, the defense sucks, but I think Romo's problem is lack of commitment to the run (by the OC and himself checking out) and being a gunslinger with a slightly above average arm. He can't make the young Favre, Marino, or Elway throws, but he still tries... lol. Somebody like that can't be asked to throw the ball 45 times a game week in and week out. He's not Brady or Brees. If someone is Dallas could figure that out he'd be just fine.