1. Andrew Luck
2. Colin Kaepernick
I think you can divide these 4 quarterbacks into two main groups. Kaepernick and Luck are group 1 that I'd put at the top. Although most Yahoo Answers fans seem to disagree with me and put these two on the bottom. Then you have group 2 with RG3 and Wilson on the bottom, which most people seem to put on the top.
I like to rate the quarterbacks moreso on what I see when I watch them play. When I watch Andrew Luck and Colin Kaepernick, they exhibit the composure and talent of veteran quarterbacks. Both are good under pressure. Both of them can make throws that I call "thread-the-needle" passes where they have tight windows to get that pass between defenders and to the receiver. And both exhibit good decision making. I'm placing Luck a little over Kaepernick because he's a little better at those thread the needle passes and last year he was the most composed quarterback in the NFL on critical drives with 7 come from behind drives to win the game. Luck also is better at having that veteran decision making you want to see from a quarterback. Kaepernick is a little more athletic, but not by much if he is. People fail to realize that Luck was like 1/100th of a second slower on the 40 yard dash than RG3 and he tied Cam Newton's time on the 40 yard dash. Not to mention Luck out jumped Newton by about 4 inches in the vertical jump. But I think Luck and Kaepernick will both be Hall of Fame quarterbacks some day.
Wilson and RG3 had the better QB ratings last year than Luck and Kaepernick. But QB ratings can be majorly affected by other things such as how much or how little the quarterback passes the ball. The less a team passes the ball, the better it is going to make a QB rating appear. Why? It often leaves the quarterback with 3rd and shorts instead of 3rd and longs. And the more you run the ball the more it takes the pressure off the passing game, leaving receivers wide open. The Seahawks had the least number of pass attempts of any team in the league. And RG3 and Wilson were tied for the number of pass attempts they made at 393.
My concern with both of these quarterbacks has been how well will they do when they are forced to pass the ball more. RG3 was forced to pass it more in week 1 against the Eagles and he got picked for interceptions 2-3 times. He also threw a lot of incomplete passes on pressure plays and his completion rate wasn't much over 50% just like Luck was last year. If RG3 had been in the same type of situation as Luck was in last year, he'd have struggled to had a completion rate as good as what Andrew Luck had. The same I think would be the case with Wilson.
Wilson is better on decision making ability than RG3. But I think RG3 has more play making potential. Watch him in that second half against the Eagles where he threw the short passes and faked running. That opens up his receivers. Wilson right now is probably a better quarterback than RG3 due to his decision making. But I think when the careers are all said and done RG3 will likely outshine Wilson. RG3 just needs to learn a few things and get smarter in his passes and be able to hit those passes under pressure.
One cool thing to note is how the 49ers even came by Kaepernick. Jim Harbaugh asked Luck who he'd recommend from the Manning Quarterback Camp. Andrew Luck told him Kaepernick. This was way before Kaepernick really hit anyone's radar. Luck liked how Kaepernick played smart and ran plays.