Not sure if this has been discussed - sorry if so and feel free to merge accordingly, but I think this is new concept.
What would be good if we could have multiple pofiles, each of which has its own multiple save points.
Each profile could have its own mods.
Mods have the ability to force a seed (new games only or they fail to load).
So profile 1 could be vanilla game, multiple save slots, no mods.
Profile 2 could be "Josh Mods" + whatever mods, multiple save slots.
Profile 3 could be "Aspmans Tutorial mod" (with forced seed), multiple save slots.
The reason I think this would be cool would be a modder could force a seed, causing everyone to be in the same system. This would allow content and missions that are specific. Thus you could create a complete storyline based game where you can make references to planet names etc.
However obviously existing players would already have their existing game, hence the need for the profiles and save slots within those profiles, so the 2 things can run alongside each other.
I suppose mod manager thing would need to be clever enough to detect that a mod requires a certain seed so only allows its install on new profiles/new games.
There maybe other ways of achieving same results, this was just an idea I had whilst thinking about modding some in-game tutorials.