You mentioned having to retune the stories option, but I think that is not true. Have you "exported" your settings? If you export your settings with story progression and/or master controller, you are able to "import" your settings later, which is a TON quicker and less crazy-making. Please correct me if I am missing something.
There’s not a whole lot that I bother changing, and since they’re spread across several different NRaas mods I have installed, it practically defeats the purpose. Mainly, I want to
1) Disable the stories brought by StoryProgression,
2) Prevent memories from being generated with MasterController, since it conflicts with the vanilla option they patched in,
3) Re-adjust the default options in Saver (15 min.) and Overwatch (8 a.m.), and
4) Remove the visual nuisances I have with PortraitPanel. (Why did I install the fourth one, come to think?)
Occasionally I’ll change other things, but otherwise they’re left at default. Does anyone else change only such a small number of settings?