This would be rather tricky at this point in progress to make a patch for, but what specific graphics did you want to be toggled?
Changes to the existing game graphics, so basically the ones you mentioned in the OP.
May need more specifics here too, though it would be easier to toggle than the graphics since all I'd have to do is change some pointers; especially considering all the minute changes I've made to the graphics over the years.
I'm referring to remixes and custom music added. I'm fine with the music changes you mentioned that you made pokemon from different regions play their region music. I'd just like to keep assets from the gamefreak pokemon games for the standard game content.
If you mean that the shiny chances could be changed back to normal, I could do that too and make it optional if you guys think I should. I've been considering removing it because many people may still not know about it and think they found a real 1/8192 Shiny, so I've been kind of regretting upping the chance to 1/200 even if it is only for a couple Pokémon.
Yes, this sounds preferable. However, I did not know about the Lapras you mentioned down below, and I do like the idea of a common pokemon like that being shiny like the red gyarados. So I wouldn't be against only keeping the single shiny Lapras, with all other pokemon having normal rates.
I can do something like the Secret Base idea but was really planning on giving the Trainer House in Sootopolis (in Mossdeep in R/S) some "DLC" trainers that either can function via patches or just show up depending on what day it is or something. I'd probably have to put this in a later release since I'd really like to make the next one available soon, and it would end up taking considerably longer. I am reluctant to mess with the Secret Base maps because the exact way they work is not really fully understood (at least to me), and I feel like it would lead to a ton of glitches.
I expected this might be tricky. But I'd definitely love it if you could look into it at some point. Effectively what I would think might be done is that you could leverage the game's existing feature to mix records that adds trainer secret bases to the game, so that work is already done for you, and the only addition would be some new feature ingame to let you "create" the record that otherwise would have come from a multiplayer connection.