One thing that always ends up being rather time-consuming for me is moving mods in and out of my GameData folder depending on what save I'm playing. For example, the Jool 5 challenge seriously limits the amount of mods that I'm able to use, so I have to remove most of the mod folder in order to play in that save, and then replace all of those mods when playing in a more heavily-modded save. I also have several installs in which I use different planet packs, and I have to change which planets are installed in which save. It all becomes quite a pain, and I'm sure most other players who use mods have similar troubles.
Anyway, the point of this thread is to question the possibility of a mod that allows each save to have an independent folder for addons, and to request that someone make such an addon if they are able to. I would do it myself (or rule out the possibility if it's not doable given the way the game is coded) but I have next to no knowledge about coding, so all I can do is make the suggestion.