Faster clock speed doesn't nessisarly mean better performance. Why is an Athlon 64 FX55 slower than a P4 3.6 in clock speed, yet it manages to beat it in every benchmark? For the gpu, there are many, many reasons ranging from the pipelines it have, to the way it utilizes the graphics driver.
6600GT = 500/500, 8 pipelines
6800GT = 350/1000, 16 pipelines