My favorite problem with franchise mode is that they finally introduced restricted free agents in '06 and left it in for '07 (I think, unless it was '05 and '06), then just decided to remove it. So three-year players can just become unrestricted free agents. Granted, I didn't like when FBs were being signed away as restricted free agents costing the teams a first and a third, but at least that facet of the game was there.
And this was so good, I just had to share on last years game...
I was only about three years in. The Falcons had just drafted a QB high in the first round the year before. In this years draft, they took another QB top in the first round, another in the second round, and a third in the fourth round. That's silly enough, but they topped it off by signing a released Tom Brady (due to Patriots cap issues, of course). I think the Falcons are OK at QB, but that's just me.