They came out with one big update that took care of almost all those major things that Trav already mentioned.
You should be able to adjust your defense if not during the season at least in the off-season.
The major tweak was that the game would run a play before the clock wound down (IE, a FG to win/tie the game rather than just lining up and letting the clock run out.)
I think the problem with this game is that they tried to sell/package it with Madden XX before you could buy the game by itself. So some people never gave it a chance even though it's 100x better in regards to the GM'ing of a team instead of the pathetic excuse that Madden has been trotting out every year.
I know the lead developer of HC was moved to the Madden team but I haven't seen any improvements to the franchise mode... but I've only bought 3 of the past 7 Maddens on the next-gen consoles.
When HC 06/7? (the one with the Chin on the cover) that was also released on the PC so I know that it's had a pretty faithful following and mod community support. It's really a shame they didn't do the same for as far as releasing it on PC.
I loved the GM'ing/franchise aspect but I couldn't stand the play-calling. I ended up simming all my games and still could go undefeated with the Seahawks three years in a row.