Go with 06.
Basic gameplay is the same except that they did add a new wrinkle to the passing game.
They also added a little side game where you can invent a person, pick an agent, get drafted and go thru your career that way. Doesn't really interest me at all, but some might like it.
Overall, not a lot of difference, but just the fact that it has the new rookies and players that changed teams added, I think it makes it better. Which is exactly why I get the new version every year.