You know what would be nice? Ingame mod managers that let you enable and disable mods as you please. It would be located in the Options section, and also checks for version compatibility. (It doesn't auto-disable the mods if they're listed as incompatible.) You know what would go really well with that? Giving your characters tags that can be viewed from the character selection. There would be a little "Tags" button at the top-right of their character bar on the select; you can write up your own tag. Examples; what if I have two characters? One is for modded singleplayer, so I'l write "ModdedSP". The other is a vanilla roleplaying character, so I'l write "VanillaRP". With the mod manager, I won't have to mess with files too much to switch between these characters.
