When I was growing up, drop-back passers were the norm. Guys like John Elway who had more than a modicum of athletic ability were the exception to the rule.
This has been changing for some time. Among currently active QBs, only the Manning brothers are as statuesque as Bradshaw, Montana, Marino, Kelly and Simms were. Even guys like Brady and Brees, neither of whom has ever been described as a "running QB," would have rated comfortably above-average in athleticism for a QB 30 years ago.
During this time, we have also seen the rise of running QBs. I believe, however, that the benefit of a "running" QB, as opposed to a drop-back QB with some athleticism, is overstated. Other than Mike Vick in his Atlanta days, I can't think of any running QBs who enjoyed sustained success without having enough skills to survive as a drop-back passer if need be.
The emergence of RG3, Wilson, and Kaepernick this year, on the heels of Cam Newton's breakout season a year ago, will definitely affect the thinking of NFL coaches and GMs. I do think we'll see a lot more running QBs and a lot more read options. I also think we'll see a lot of failures, because most of those teams will not find a QB with the preternatural talents of RG3, Wilson, Kaepernick, and Newton. In the long run, I think we'll find that guys with elite running ability and solid drop-back skills are as rare as drop-back QBs with the skills of a Peyton Manning or a Tom Brady.
The only difference is that the running ability is easier to gauge than the soft skills that make for an elite pocket passer. Teams might be more willing to gamble a high draft pick on a running QB than a traditional one. This means guys like Wilson and Kaepernick will go in the first round in the future, and the next RG3 might get drafted ahead of the next Andrew Luck, but I think this will have a marginal effect on the games we watch on Sundays -- good running QBs will continue to be the exception to the rule.