According to espn.com's Average Draft Position chart, thirteen of the top 14 players picked in fantasy have typically been running backs. I have not played fantasy football in a few years, so I can not speak to the wisdom of drafting Willis McGahee before Tom Brady or Carson Palmer. However, I am quite certain that there is not a general manager in NFL (not even Matt Millen) that would make such a choice for their real team.
I have always been a stickler for reality in my sports video games. As an adolescent, I preferred playing Madden NFL and NBA Live to NFL Blitz and NBA Jam. Perhaps that makes me a bit of a Stu. I don't care. I like sports as they are, not as if they are taking place in some ridiculous alternative universe.
Similarly, I want fantasy sports to be as realistic as possible. I want fantasy players to be valued in direct proportion to their real value on the field. I understand that the complexities of football make such a translation nearly impossible. More than any other sport, individuals are extremely interdependent in football. So yes, fixing fantasy football would be a massive undertaking. But shouldn't we at least try? ESPN's cheat sheet recommends choosing Joseph Addai with the 6th pick (before teammate Peyton Manning) in the fantasy draft. In real life, if the Colts were contracted, he might be about the 6th guy taken off of his own team (after Manning, Freeney, Harrison, Wayne, and possibly Bob Sanders). Fantasy football has almost relation to the sport it's modelled after.
Fantasy baseball has it's own issues as well. It overrates baseball stealers and closers. It undervalues guys that walk a lot and middle relievers. They still haven't made an adjustment for naturally inflated AL ERAs and defense is irrelevant. However a fantasy baseball draft will never have something as silly as 13 2nd basemen chosen in the first 14 picks. Fix fantasy football. I get bored in the fall.