Why don't we just see what people that aren't Seahawks or 49ers fans think? I took the liberty of Googling it, but only starting after the Super Bowl, which benefits the "voting" for you guys, since Kaepernick made it to the big game. Virtually everything I found that ranks QBs puts Wilson ahead of Kaepernick.
http://mynorthwest.com/275/2199596/Seahawks-2012-draft-picks-rated-tops-in-new-review (Don Banks choosing Wilson over Kaep at bottom)
Now, since it's only a window of 6-and-a-half weeks of articles to look through, it's kind of limited compared to what's available if you just Google it with reckless abandon. (Excluding biased sources, as well; such as Bay-area and Seattle-area writers, etc.; and before anyone jumps on the mynorthwest.com URL, it's talking about something Don Banks with SI said.) I found one spot where someone ranked Kaepernick ahead of Wilson, (you find it ) but virtually everyone, everywhere, puts Wilson ahead of Kaepernick.
I'll be curious to see how this gets contested. Talk about a slightly faster 40 time, or top speed, (both of which are side-stats for QBs, anyways; they are passers, first and foremost) or what you think so-and-so will be able to do in the future, but the consensus is Wilson's the preferred QB as it stands currently.