Some things I've noticed that either haven't been discussed here, or I just haven't seen:
1. Facemask penalties being called on human-controlled defenders consistantly when they try to strip the ball (R2 on a PS2 controller) even if their hands go nowhere near the ball carrier's facemask.
2. No updates to the spoken names in the 09 edition for the PS2. (I play with the Browns - Pro Bowl returner Josh Cribbs still simply "Number 16" in Madden play-by-play, and Safety Brodney Pool is frequently called "Hope" instead of "Pool" when the play-by-play guy calls him by only a last name.)
3. Teams that have rookies and/or young players who are clearly the future of the team at their position(s) in real life are kept in a backup role, and thus do not progress, in Madden because the CPU does not take age and potential into account when setting depth charts. (Joe Flacco has been beaten out by Troy Smith in every franchise I've simulated, Ryan Torain never gets to start for Denver, and DeSean Jackson is usually relegated to a third WR role with Philly. I could go on, but you get the point.)
4. Teams sign FA they don't need. I can't even count how many times I've seen CPU-controlled teams with 2 or 3 Pro Bowl-caliber QBs or RBs on their rosters eating up cap space as backups simply because they were available as FA. The same is true with draft picks - teams will either pass up no-brainer "best available" types in order to draft a TE, K, or P to fill a roster, or they'll draft a top-5-projected QB when they've already got a superstar in his prime on the roster.
5. There's no allowance for "trick" formations & "slash" players - you can't put a WR at RB, a RB at QB, etc. It's stupid to be forced to use a P or K as your emergency QB when you've likely got a RB or WR on your roster who played QB in college and has decent THA/THP ratings. (Hopefully this be fixed next year due to the popularity of the "Wildcat" formation this year.)
6. Lastly, this is more an indictment of EA's
PR team than the development team: there were a lot of new features touted before Madden's release this time around that were not included in last-gen versions (like my PS2 version). I understand that they can't include everything because they may require more robust systems to operate, but they never mentioned this in their press releases to my knowledge. They could at least be honest with the consumers, and let us know before plunking down $40-50 for a roster/soundtrack update that we're not getting anything truly new unless we also plunk down $400 for a new gaming system.