Even a rudimentary system would be of enormous help, an example I can point out is endless space, a game whose modability was frankly limited but still better than GC3's overall.  And this was largely due to a simple dependency system.  You listed in the header for the mod those files the mod had dependency on, then you could build your files as you saw fit. If for example you were modifying ship components and wanted to overwrite a specific component you did not need to replace the whole file. You simply made sure the internal name matched that of the original item and the file header listed the correct entry type just like we do currently, but instead of throwing duplicate entry errors and acting all weird in game, the game simply over-rode that entry and it prevented the modders from needing to create total overwrites anytime they wanted to replace one thing in an original file.