As long as NMM retains the option to sort loading order it will be better. It's also way easier to know what you have downloaded or not. But devs must keep a competitive advantage, for a starter it would be nice to add the possibility to add folders in the mod list, set up loading priority from the mod list, and being able to move up/down the mods in the mod list. If they add these sort of features NMM will still be way better, right now Steam workshop is a mess for complex mods which require installation, overwrite stuff, etc.
