I’ll second this method for the Skyrim Special Edition. Works for me, although I don’t have an extensive mod list. Just:

SKSE, SkyUI, Vilya in Skyrim, Unofficial skyrim patch, Achievements Mod Enabler.

Will be moving to the new Nexus app when it is out of alpha or enables Bethesda games.

For Oblivion, I’d do something similar.

For Morrowind, you should use OpenMW and install mods through that as they describe in their docs.