I test rode both the same day along with a CAAD8, Six13 and a BB30 Synapse SL.. The SystemSix is superstiff and super responsive. It would be my first choice if I was only going to ride on glass-smooth roads. The SuperSix was nearly as responsive but had a smoother ride - it was my favorite of the day. It was out of my price range at the time and I ended up with the Synapse. But after a year of saving my pennies, I finally own a SuperSix and plan on keeping it as my primary road bike until some breakthrough makes carbon fiber frames obsolete.
My two roadbikes are the SystemSix and the SuperSix. (Before the SystemSix I had the Six13.) I have extensive miles on the System and Super -- thousands on each, I've lost track how many.
SystemSix -- headtube, toptube, downtube are monoocoque carbon; rear triangle is all aluminum -- is arguably the stiffest bike you'll ever ride. Explosive for sprinting and an excellent climber because of that all-aluminum bottom bracket and rear aluminum triangle. On descents it feels like you're on a rail, no twitching on the front end. The negatives are that it's a little harsh (compared to the full carbon SuperSix) on the all-aluminum back-end if you're going over bumpy roads, and it's not the lightest frame in the world because of those beefy tubes on the front triangle. I spoke to an Italian ex-pro who road on the Barloworld team (and other teams and thus other bikes) and he said the SystemSix was his favorite bike for racing, hands-down. I generally use the SystemSix for crit racing because of the stiffness and for club rides that are going to be super-fast because I have my aero wheels set up on the System.
SuperSix -- all carbon -- is a terrific blend of stiffness AND smoothness. And while it's not sub-1KG in weight like the Scott Addict or the Cervelo R3, it's still relatively light. I have ridden a couple of all carbon racers and the Super is definitely stiffer than them. (For example, last week I rode the quite-expensive Wilier Cento and while incredibly light and silky smooth, it felt like a noodle compared to the SuperSix.) The Super is not as stiff as the System, but for every day training on smooth and rough patches, it's an outstanding bike, it will still sprint solidly, great on corners, it's a good climber, and you will feel fresher on long rides on the Super compared to the System. I generally use the Super for everyday training, road races, and long club rides/metric centuries, etc.
As of 2008, both bikes were made in the Pennsylvania factory. The System is no longer in production effective the 2009 line, and starting the 2010 line I understand the Super will be made in Taiwan. My two cents is buy the 2009 Super or the 2008 System before the "HANDMADE IN USA" stickers on the seatstays disappear on future Cannondale models. It's a point of pride for me. Just my personal opinion.
I agree with what fueledbymetal and fornaca68 said. I just bought an 07' NOS system 6 this week and did a lot of test ride on it and also a super six. Although the super six is a noticeably smoother ride, I just can't resist the "wow" factor from system 6's rear aluminum triangle. With a set of tubeless tires system 6 should be comfortable enough for a long ride.
I have a System six and love it, I was thinking about going back to a CAAD 9, but I think the System will do me for a while. I had the chance to ride a 2009 Specialized SL2 with DA 7900, now that is a STIFF bike around the BB, easily stiffer than the System. But alas at around 10k AUD way out of my range.
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