If it matters much, the 2008 Six 13s have a new seatpost size - 31.6. In fact, I think most of the seat tubes on all their bikes have gone 31.6 after being 27.2 for so long (System Six and Super Six are definitley 31.6.
The head tube of the 08 System Six is also a little taller for comfort (as explained by a Cannondale rep at a race).
I'm an 06 Six 13 owner and 07 System Six owner. Love them both, but the System Six is definitely a lot stiffer and just beefy. It feels like it weighs 1-2 lbs heavier, but it's around the same weight (both come in around 15-16 with 1500 gram wheels). I think I get faked out by the FAT tubes of the System Six.
I test rode a Super Six for kicks and it was a nice riding bike, but really felt like it was no different from riding my System Six, despite completely different rear triangles.
I'm a Cannondale fan, as I also have their touring bike. They fit me right and simply haven't gone wrong with my body and riding style yet...