I'm having some issues with players on special teams, when playing with a team that runs a 3-4 defense in Franchise mode.
I play franchise with the Ravens and my starting MLB (2nd string according to Madden) is playing on kick-offs, which fatigues him before my defense takes the field and forces him to be subbed out rather quickly. And at the same time my 3rd string MLB (#4 on the depth chart as I'm playing 3-4), who should be playing special teams according to Madden, hasn't appeared on special teams all year long and I'm 15 games into the season. You can check this by looking at Career Stats -> General -> Downs Played.
I wish Madden 10 used special teams players on special teams