My experiences were the same - I was getting awful FPS (with a 660Ti) until I re-installed the cloud and water textures, and I had the REX Textures installed for clouds and water which would appear to have been the culprit.
You could try this which worked brilliantly for me.
Replace your cloud textures (use the 512 or 1024 not HD) from here:
http://simviation.com/1/search?submit=1&keywords=hde+ (choose second download on page),
then install 'Oscar's Clouds' v4 from here:
Backup cumulus01.bmp from your FS textures folder before you do.
I don't know who Oscar is, but I'd like to thank him for his texture excellence!
FPS were also awful if I had Water 2.x Low selected, until I installed these textures:
Water - http://flyawaysimulation.com/downloads/files/1457/fsx-water-effects-texture/
Also, I found that when I set anisotropic filtering to application controlled, rather than the recommended user defined/off I got much improved FPS. This goes against the grain of the experience of many, but it's worth a shot if you're still having problems.
Hope this is helpful to some of you. I'm really happy with my sim now, for the first time in a long time. Thanks to all for the DX10 goodness.