Is there a way to have separate save folders per user like there is in pretty much every other game I have played? All the saves seem to go into the same date-oriented list with no way to distinguish who played.
Savegames are already separated by Steam account. Because saves are synchronised with the Steam cloud, there is no way to separate them beyond that.
Seeing as you are not allowed to share a Steam account, as lunboks already pointed out, this should not pose a problem.