What is the penalty for keeping each guy? Assuming all things are equal, McFadden would really be the obvious choice.
Best Case Scenario:
McFadden plays the whole season and continues his momentum from last year: Top-5 RB
SJax plays the whole season and doesn't loose a step: Top-10 RB
Worst Case Scenario:
McFadden misses 3 or 4 games and Bush takes some TD's (Similar to last year): Top 15-RB
SJax goes the way of Sean Alexander, Clinton Portis, Edgerrin James, etc: Top 30-RB (and not even on your team by year end).
FF is all about maximizing you chances to win, considering both Best and Worst case scenarios are better for McFadden, since the reality will be somewhere inbetween, it's more likely McFadden gives you the better season.
Of course, this is assuming both guys cost the same to keep. I have to decide whether to keep McFadden for a 6th Round Pick, or Miles Austin for a 12th Round Pick....ughhhh