I know we're just rehashing the same old with this, but there's also a big difference between college and pro success. There are players--Reggie Bush and Vince Young are good examples--who are spectacular in the college game in a way that Tom Brady and Aaron Rodgers couldn't be. In the college game, coordinators look to exploit athletic imbalance. In the pro game, there isn't much athletic imbalance, so the focus is more on precision (against a very high level of athleticism). So in the college game, a quarterback who can run all over the place evading people who aren't as athletic as him is spectacular. In the pro game, a quarterback who can consistently put the ball in precisely the right place, while shifting in the pocket to gain 3/10s of a second of time to get that pass off is much more important.
One of my favorite examples will turn your stomachs, but I'll use it anyway. As much as no one here will like it, Jimmy Clausen was a phenomenal college quarterback. And thank goodness for Notre Dame because as bad as it was with him, without him those Weis years would have been much, much worse. He was a smart quarterback who could really take advantage of athletic imbalance (his receivers', not his) when picking apart secondaries (with Weis's help). But in the pros he just wasn't big enough, strong enough, or fast enough to keep up with the elite athletes that are on every team. His smarts couldn't make up for that.
And that's (at least one reason) why the pros draft on size and strength. While there are exceptions, few players are able to make it in the NFL without the base level of athletic prowess that permeates the league.
Now, to the Oklahoma QBs who are winning the Heisman these days? They are system quarterbacks. The system, though, is--in part--to recruit better athletes than the teams they play, and put the ball in their hands as much as possible.