here's a few things I would like to see...

-ST Coach - After a decade or so in franchise mode, all the ST coaches suck. This should be improved.
-Stadium Upgrades - most of them are meaningless. Make more of them help out your team, like the ones that reduce injuries. Maybe better training equipment will develope your players faster, etc.
-Training Camp - This really needs some changes. Trench Fight has been extremely hard for too many years. They need to allow more time. And I don't know about everyone else, but the Precision Passing is much more difficult this year. My QB never throws the ball in the same route twice. No matter how hard I try to use the new "precision" technique, I can't hit the d*mn circles. There is no consistency to how the QB throws, so you can't learn the patter and improve. For me, this drill is impossible.
-Signing Free Agents - does this have to move so slowly? It takes forever to increase or decrease your offer. For some reason it's faster when signing your draft picks, but extremely slow when signing a FA. Please speed this up.
-Soundtrack - It's not bad each year until you've listened to it FIVE THOUSAND TIMES. I don't connect my PS2 online, but I would if I could download an updated soundtrack every so often. Hell, I'd pay for it just to switch it up sometimes. I end up listening to more music on Madden than the radio or online.

Overall - my top beef is with the training drills. It's fun to improve your players, but very frustrating when a drill is just simply too difficult or requires more luck than skill. I like the idea too of allowing you credits to increase the player's abilities based on other factors in addition to the training drills, like mid week drills, how much money you make, your training equipment, coach, etc.