I've seen every carry of Felix Jones career. I've seen him play in person 16 times and seen the rest of his games on tv. I might not be an expert on much but I know a little bit about Felix and Darren.
Felix did NOT simply pad his stats by running against tired defenses late in games. His yardage and big plays were fairly evenly distributed throughout the 1st and 2nd halves and throughout the early and late season games. I'd be shocked if you could find any trend to support that argument.
He did NOT get easy yards because defenses were so glad McFadden was out of the games, they just rested. That one keeps getting repeated and is pretty ridiculous.
There is some shred of truth, however, to the "Felix was only great because of McFadden" argument. The formation where Felix got the majority of his big plays was the Wild Hog. This is the formation I'm sure you've all seen where McFadden lines up in the shotgun and takes the direct snap. On these plays, Felix is sent in motion so he's close to full speed when the ball is snapped. Defenses are forced to pack the box tight to stop McFadden from running up the gut. When they do, DMac hands to Felix (who's in a dead sprint) and Felix easily gains the edge and gets to the outside. While Felix still does amazing things once he gets in space, there's no denying that if not for defenses keying on McFadden, Felix couldn't get in space so easily and so consistently.
So I don't buy into the "tired defenses" or "resting defenses" arguments at all. But there is no question a large part of Felix's success is thanks to McFadden.