The Six13 gives a slightly smoother ride IMO. It was Cannondale's top of the line, but I remember reading someplace that the CAAD9 is ligher. Here is the story with the Six13, the 2008 model is a one-off but all the others are basically a CAAD frame with carbon tubes interlocked, usually in the top-tube and down-tube, but in earlier years also in the seat-tube. I believe that the models with the carbon in the seat-tube were said to be less stiff, or felt noodle-like (I *think*, i'm only going from what I *think* I read). The bare aluminum finish while beautiful looking sometimes will have cosmetic corrosion where the carbon meets the aluminum, not sure if it's a structural issue or not. In short the Six13 up to 2007 was CAAD based with Carbon interlocked tubes for a smoother ride, was near the top or the top of Cannondale's lineup.
The 2008 Six13 ended up with a frame that has a slightly taller head-tube than a corresponding CAA9. The rear is also not identical to CAAD, but appears to be from the SystemSix. Also for 2008 the tubes were no longer interlocked, but instead bonded together (and are painted over where they meet). This frame was only made for a single model year, although i've read that it's supposedly very stiff.
The SystemSix is Carbon with Alu. seat tube (bottom bracket area I think) and seat stays. I believe the System Six and 2008 Six13 are the same except that the SystemSix shares CAAD geometry with the shorter head-tube, and is all carbon, while the Six13's front is Alu and has the taller head-tube.
I agree that CAAD9s fetch a premium on the resale market, you're better off looking for a 2010 or 2009 leftover if you can find it brand new. Otherwise consider the Six13 or SystemSix, they share much of the CAAD9s heritage but have some carbon added to them. All three are highly regarded. My guess is that more labor was involved in the Six13/SystemSix manufacturing and they were discontinued in favor of full carbon which is easier to market/sell.
AvantDale: WTH is that? I don't think i've ever seen a Six13 with only carbon in the downtube?!? I thought it was seat tube + top tube + downtube for the first year, and then downtumbe + top tube afterwards? Maybe that one is older and i'm wrong.