They've been selling far more copies of the PS2 version than any other version. So they probably won't change the way they develop.
Regarding this thread, Madden 2006 will come out for the current consoles in August 2005. But just before Xmas 2005, the Xbox 2 is suppose to be out.
So will EA support the Xbox 2 launch with a Madden 2006.5? If it does, I can see them using the current engine but scaling up the resolution to HDTV resolutions. In other words, much prettier graphics with the same gameplay, much like the PC version is today.
But even when they do a "new" engine with the new consoles, the gameplay will probably be similar to what we've seen since at least Madden 99. There will still be speed cheats, unless they fundamentally change the defensive AI to position the defenders better.
An EA guy claimed with the next generation that everything you see on screen will be modeled, meaning real-physics rather than motion-capture animations determining the outcome of each event.
But he's probably talking about different kinds of games, not sports games. Ironic, since sports games are what EA is known for.