It actually is a bit different. What you want is a mod manager in the game, right? Easy to select what mods you want. What I'm talking about here, what DataZip.exe does, it's the backend to the XML - how it gets put together, interpreted. Although a fixed-up DataZip.exe could potentially enable us to put all mods in /mods/, it wouldn't make it easier to manage the mods the way you speak of.
But they go hand in hand, this would just have to come before. There's no point in a mod manager as long as people are modifying the installation directory. I'm doing it too, because I have to, because of the bugs in the linked topic. I also have huge parts of the Background Unitstat mod disabled because I can't do it without putting it in the installation directory.
