Well I'm sure there are a few minor upgrades to work all the bugs out.....but the one that sticks out most in my head is where the 04/05 models have capped nipples on the intake manifold, the 06 models have tubes on those nipples that connect and run up to the oil fill tube. I've heard that this is another safeguard against flooding. I've had my 06 for almost 3 years now and it has never flooded (knock on wood)......and yes I've had one or two instances where I moved it without it warming up and shut it off cold. (Simply because I forgot)
This is is a good thread to see the changes each year----->
http://www.rx8club.com/showthread.php?t=143280