A few things (Follow the steps/suggestions in this order):
1) Don't assume that because your mods worked OK with previous patchers that they will work ok with new patches. The TESV.exe, the update.esm, and update.bsa were all updated, so any mods that rely on the ESM and BSA will need updating, and the EXE has had some engine changes made as well. Check all your mods for updates and try again. Post your loaad order as well.
2a) Skyrim is not restricted to 2GB of RAM, the LAA flag is still on the executable, so something else is going on here (32-bit OS's are still restricted to 2GB RAM though). Make sure all your drivers are up-to-date and post your systems specs and Dxdiag (In spoiler tags please).
Edit: 2b) Try the "Verify Integrity of the file cache" option.
3) Have you tried deleting the Skyrim and SkyrimPrefs ini files in your My Documents/My Games/Skyrim folder? These should be deleted after every update and after you update drivers to ensure stability. Run the Skyrim launcher and then run the game once to generate new ones properly, and then try going to Riften again.
4) Uninstall all mods that you have running for SKyrim. (Deactivating the ESP/ESMs is not enough, as scripts will still run if present in the scripts folder). Once you have done this run the game, make a clean save, quit the game, and then run Skyrim again and load that save and try riften again.
5) The game could be crashing in the Riften area due to a corrupt spawn, this has been an issue since the Oblivion days, so the fact that it happened after updating to 1.6 would just be a coincidence. The only way to fix this is to go to an isolated cell (coc qasmoke) and wait for 31 days so that the respawn timers can reset. Then use the coc command to leave qasmoke (coc whiterun for example). then attempt riften again.
These are all the options you can try (off the top of my head anyway). Naked enemies? Sounds like a mod is changing ARMO records, so it needs to be updated (If you have the USKP update to 1.05B as the patch changed quite a few things that messed with the USKP).
Edit: As a LAST RESORT ONLY, back up all your saves, uninstall Skyrim completely (make sure to delete the Skyrim and SkyrimPrefs ini files as they are not removed when Skyrim is uninstalled), run a registry cleaner (CCleaner is the safest option I would recommend), make sure the skyrim directory has no files left behind, and then do a reinstall.