I have an SSD, and usually Skyrim loads in a few seconds and runs at a smooth 60 fps with my 560Ti GTX and i5 2500k. I updated, and initial load is like 2-3 minutes, and framerate is around 5-10 fps. I do use mods, but I tried the following:

- Deleted my skyrim.ini and skyrimprefs.ini and let the game generate new ones.
- Ran the game both through SKSE (updated both this and ScriptDragon today, they are made to run with the new patch) and through the Launcher
- Ran the game with all mods unchecked

and finally

- Removed ALL mod files. Started a new game without any mods, without ScriptDragon, without SKSE, with no .ini edits at all and...

Still the same results. Anyone have the same problem?

Not enough. You need to completely uninstall the mods.

I did that. I removed every .bsa and .esp except the "Skyrim" and "Update" ones, and still the same result.

Did you remove the loose files that are associated with your mods, such as scripts?

It seems I fixed it by updating my graphics driver, although I already had the second newest one.