I had this issue up until last night.

I had previously been using a Zotan GTX 260 and running Skyrim on custom Ultra settings with hi-res textures. I switched to an Asus GTX550 ti and found a huge hit in FPS, even with High settings.

I updated the drivers but it was still massively underperforming. Couldn't figure this out so I went throught the forum last night and struck gold. I really wish I could find the post so I can thank the person who suggested it, but the solution was to remove the bundled Asus utilities that came with the card and reinstall the drivers. I don't know why, but it worked. I also deleted Skyrim's ini file and let it create a new one.

I'm now running on Ultra settings with everything turned up. I've turned off AA as this was causing a bit of stuttering still, but from what I've read on here, some people are saying that the AA doesn't really do very much anyway.

To anyone in this fantastic community who was tearing their hair out over this as I was, I hope this helps