While the convenience of Steam Workshop mods auto-updating is nice, I've also had some issues with it where it continues to download mods for games I no longer have installed, so Nexus is nice for a more "manual control" approach for mods. Also, managing dozens of mods and sharing those mods with friends can be quite cumbersome with the Steam Workshop.
Despite all that, I think the Nexus and Workshop can co-exist, since the Nexus is nice for finer control over your mods, and the Workshop works well with a "subscribe and forget" mentality.
