In my staff dynasty rankings dated 2/23 I had Wilson #10 and Kaepernick #11.
In my update this week I switched them, Kaep #10 and Wilson #11.
If I wake up in a different mood tomorrow I may switch them back. I see it pretty much as a coin flip right now.
Wilson had a full season and showed as the season went along that he gets it and is going to be a good one. Being a running QB helps, and adding Harvin has to help too. But, as long as Carroll is HC and they have a strong defense they won't abandon the run and start throwing for 300 yards a game regularly like some teams do. So, he's a low end dynasty QB1 (#10-12 or so) at least until I see evidence that causes me to move him out of that range.
Kaep as we all saw in the playoffs has potential to be great, Harbaugh hand picked him in the 2011 draft and he has I think a higher ceiling than Wilson if all goes well. But he only played part of a season and has potential to be more erratic than Wilson, with a lower floor. I don't think he'll have quite the completion % over time that Wilson will have. His team also has a stout defense and a coaching philosophy that emphasises ball control and won't toss it around like crazy either.So, if you want maybe a higher ceiling but also a lower potential floor, go with Kaep. If you want a pretty dang good steady QB but likely without elite fantasy potential, go with Wilson.
Just one idiot's opinion.
I think this is the thing with both players/teams. I agree that both of these players should likely be right next to each other in rankings and it is probably a waste of your researching/scouting time trying to pick one over the other. Overall, I think BOTH are overrated in dynasty due to the bolded part and the oddities that occurred last season for each team. In general, I would slide both down to wehre they sit in the 14 & 15 range as dynasty QBS.
In an inexact order, I would place them under:
-Rodgers
-Brees
-Newton
-Brady
-P.Manning
-RG III
-Stafford
-Romo
-Ryan
-Luck
-E.Manning
-Rothlisberger/Cutler/Rivers
-Rothlisberger/Cutler/Rivers
-Kaepernick & Wilson
For various reasons, most of them proven history, I think in the next 2-3 seasons, there is strong evidence to suggest that every person above these guys on this list will either straight up outperform them or it will be so close that it is not worth paying the price it will take to get either guy.
Don't get me wrong, I think both are bright young stars in the league and over the course of 5+ years, it may be different. However, so many things in the NFL change so quickly that it is usually not smart to predict things past a couple of seasons (if we were having this discussion 2 years ago, the guys at the bottom of this list in Big Ben, Cutler, and Rivers would have all been in the top 5-6 and guys like Vick and Bradford would have made the list...things change quickly.)
But at the end of the day, with the style of play of the teams and long term uncertainty, and unless you are in a 16 team league, I'm pretty sure it is not worth the price.