Its gonna be a LOT of work, especially with some old mods that require ancient game versions.
First of ideas is to refuse to use mod system and modify original core files. Its much simpler bc u need less comparing and code looking, updates can be easy, come with lot of changes. If they change same string, it can be managed through checking for additional conditions. Adding new strings is no problem. This is my preffered way.
Second, is create sequential list of mods, which need to be activated in strict order, no new from outside can't be added without lot of work. They can be updated separately, but require more time and effort. If they change same string, it can be managed through checking for additional conditions. Adding new strings can be problem, bc mod system insert new string after appointed number of strings in function, which can be changed by adding new string from previous mod and possibly making new string placing wrong, which lead that all mods that use mod system, and placed after afforementioned mod, need to be changed in the spirit of additions.
Btw, there is come another questions: Do we really need all existing mods in one game? Isn't it not only breaking ballance, but also add content, unpleasant for some peoples, or totally useless?
Its a good idea to gather in one place all goods, but as ppls say before it need, lot of hard work, free time, and willing testers. Also, list of mods need to be discused and found a place for uploading changes(like github).