If you'd only like to see an explanation of why you should be downloading mods manually, skip on down to section #3. I'll first briefly explain how mods installed from the Workshop work, then detail situations where using the Workshop is sensible before explaining why using the Workshop is generally not a good idea. I can't count the number of issues I've had to troubleshoot as a result of the Workshop and I know its systems and limitations in detail, so I feel fairly qualified to explain what makes the system inadequate compared to the standard methods the community uses for mod installation. Holocron requested that I go into some general detail for the community about why the Steam Workshop is generally bad for modding, both to have all the issues laid out and easily referenced, and to clarify some common misconceptions.