I have a few mods installed on my KSP at the moment - about 10 I think. However, while I may use a certain mod in my main sandbox save, I don't use that mod in my career save. So my idea is that each savegame has its own mod folder, and they can each have a completely different mod set to each other. This would mean that you could have super-modded GPP on one save and totally stock on another, essentially removing the need to have multiple installations of KSP.
I'm not a game developer by any means, so I'm not sure how it could be made to work, or if it would be at all possible. But it would be great.
Any thoughts??