I'd also like to throw my voice behind this one. Having the player data cleared of unloaded shortcuts is really frustrating when I want to quickly load up vanilla to check some process against the wiki or work on developing a mod.

Save-specific player-data would be very nice, but I'd gladly settle ...

The in-game Mod Manager is really amazing, but it's missing a few features I'd consider critical that I'd love to see. If anything, it being as good as it is is almost a problem, because unlike most games, I've never seen significant efforts to create a third-party mod manager that would solve some ...