Not with Nexus Mod manager, it works for Morrowind, Oblivion, Skyrim, Fallout 3 and Fallout New Vegas. It installs the mods automatically and makes backups from files you overwrite so when you uninstall a mod the files you overwrote from another mod automatically jump back to their original place. It also notifies you when a mod you have downloaded has a new version.
The only difference is that you have to manually keep your mods updated, with the advantage that the Nexus has many times more mods than Steam Workshop.