I like to fiddle with mods myself and Nexus does not let you do that easily.
How so? From my experience, Nexus makes it trivial to open the specific folder for a particular mod and edit the files within. And you don't have to install mods from Nexus. You can install them from a local source without any issues. Reapplying mods is also not a problem.
I fail to see how this is actually easier using Steam Workshop?