I am not sure I understand - I can't think of any modable game which does not have a simmilar system in place. Take Oblivion, a VERY modable game - a custom mod manager had to be written by the community precisely for the reasons you describe, to mix and match mods. Even with that, if two mods modify same files, they can not be played together at the same time.
The third party mod manager for oblivion only helps to install mods without conflicts, oblivion itself will run multiple mods and depending on the order the mods load the latest mod will overwrite any conflicting mods that is loaded before it, you just have to modify the load list. The mod manager only helps to detect conflicts and helps to install mods in a certain order so users don't have to manually edit the load list, and i think the latest version of the mod manager will even combine conflicting mods files such as the leveled lists etc, etc or this may be a seperate program i'm not sure it's been a bit since i modded in oblivion.
something of this type of tool will probably be needed with sins also, i know of a generic mod tool that is designed to work with multiple games which when i get home from work i may test this tool out for sins and see if it works. But my point remains about the mod folder is useless all it is there for is just to use up space since every single gamefile will have to be copied over to the mod folder, might as else just modify the original files with a tool that will back it up before each mod is enabled with the tool.
Example
mod 1 with tool back ups all original files,
mod 2 with tool back ups all files modified with mod 1
mod 3 with tool back ups all files modified with mod 1 & 2
and so on, all the while watching out for conflicts between all mods enabled.
Only catch is to uninstall you just uninstall mod 3 first, then 2, then 1, and you are back to original. This is the way most third party mod enablers work, atleast the ones i've seen.
