IIRC, Kaepernick was the only QB to have consensus approval in Seattle's war room the year he was drafted. Dalton was graded a bit higher by JS, but Dalton had his detractors. It's pretty neat to think about it- if Seattle had succeeded in trading down a few spots and things had fallen a certain way, it's very possible that Kaepernick could be our QB right now, and Wilson would probably be in Philly with Andy Reid who'd probably have kept his job. And we'd all be saying "what ifs."
If we had Kaepernick I'd be fine with it. That said, I'm not sure Kaepernick would work nearly as well for Pete. Pete's Mr. conservative on offense- he really does need a veteran/smarts type QB to lead his offense. Harbaugh is much more daring and much better at tuning an offense for his QB. Luckily for us, Wilson is an elite talent that happens to fit Carroll's tendencies like a glove. Kaepernick wouldn't. I still think Kaepernick would be decent for us, but he'd probably end up more like Josh Freeman or Tarvaris Jackson than what he's become in SF.