According to nfldraftscout.com... Colin Kaepernick was the 7th rated QB coming out in 2011. Behind QBS such as Gabbert, Locker, Mallett, Ponder, Dalton and Newton.
Joe Flacco was rated behind Henne, Brohm and Ryan.
The point? That the two qb's in the superbowl this year were not as celebrated coming out of college as Luck and RG3 and their teams are doing just fine right now. These two teams built a solid cast around their QBs (especially defenses), molded their systems to maximize their QB's skill sets (SF even changed offensive philosophies in the middle of the year) and turned out to beat a HOF QB on one side and arguably one of this years hottest QBs on the other.
Geno or one of the other QB's coming out might not be the 2nd coming of Luck or RG3... but with Reids history of getting the most out of his QBs, I am willing to sign on to whatever coarse of action he takes.
Besides, there is no guarantee that we will even be in a situation next year to draft a QB who might be rated higher than Geno, Glennon or someone else. And like I mentioned above, even if they are rated higher, that doesn't automatically mean they will have a more successful career.
Don't' over think it... draft a QB with the 1st pick and then go BPA.