Heyyo,
Yeah, the pipelines and the bitrate impact preformance more than how fast the clock cycle is. I mean, on me old 3dfx, an increase in 60MHz only gave me like, 3F/S extra at the most... needless to say I tried higher (hey, I was a comp n00b and I thought I was "uber 1337 d00dz") and that card diddn't last much longer.. lol.
I dunno if the core of the 6600gt and the 6800 are different, but I bet they would be. An in the end, for vidcards? the better the core? the more likely it'll take onna vidcard with a weaker core.
I'm sure the 6600gt would run great on BF2 since it is nvidia-optimized. If it game off low framerates I'd be shocked. Remember to upgrade your nvidia drivers to the latest ones to get you as close as possible to 100% compatibility.