Tim,
I have all three and here is my personal opinion on each. Hopefully it helps.
2004: Good game, but it really needs the offense toned down and the defense boosted through sliders. I mean, if you play a game with 5 minute quarters right out of the box you could see scores like 48-35. For some reason I never really got into this game (I played the heck out of NCAA 04 instead) and even now have trouble going back and playing it because there are really very limited presnap adjustments on offense and defense. The special teams did work better. However, I saw too many Kick off returns for TD.
2005: I really enjoyed 2005, but the big killers for me on this one where the run blocking (the guards/tackles don't pull if someone is in front of them) and lack of penalties (I never, never saw a PI in this game). The punt returns really aren't that much better in this one than 2006. I recently put it in and went into practice mode to see how it was different and my blockers still don't block. The difference was the CPU punted the ball further so you had time to make something happen. I did come up with a good set of sliders though that made this one fun.
2006: I really think this is the best NFL football game I have ever played. Other than the punt returns issue, I think it plays great. I love the running game, the vision/precision. I have also found a way around the punt problems. Here is what I do: I have maxed out CPU punt length and I always return using Punt Block Man. I can usually get around 10 yards a return and I have actually returned one for a TD. For the CPU returns, I use the Max Protect Punt formation and I unless I am trying to pin them inside the 20, I bump the arrow down two clicks. This lets the CPU get a more realistic return average.
Anyway, sorry for the long post, but hopefully something here helps.
SF