In the case you represent above, I actually think it's more of a toss-up.  I could really go with either, but someone were to hold a gun to my head, I think I would go with Brees.  

For one, he's been pretty impressive in his career thus far.  He had that shoulder issue just over a year ago and no one knew if he could come back, but he did.  Not only did he come back, but he improved upon pretty much all of his numbers across the board.  As long as his shoulder continues to hold up, he's a franchise QB.

Frank on the other hand has a bunch of things going against him.  For one, the average career-length for a RB is fairly short, in comparison to a good QB.  Frank is at an even bigger risk, as both of his knees have been surgically repaired.  Combine his injury history (dating all the way back through high school AND the U) with his hard-nose running style, it'd be hard to make him the centerpiece of any team.

Taking a franchise QB, if you have the chance to, should be the priority in building a team.  Not that he's an expert, but ask Mike Nolan.  He passed on guys like Ronnie Brown, Cedric Benson, and Cadillac Williams to take Alex Smith (who was arguably lower on most team's big boards than those three backs).  Smith, like Brees has the intelligence (even more so, actually).  Brees knows how to use those around him to his advantage, and the hope is that Smith develops the same way.

So yeah, in short, I'd take Brees.