This is an idea for a rule where, instead of each Map's Palette affecting CSets 2, 3, 4, and 9, with the additional data in them being used for Dark Room colours, they now affect CSets 0 through 11, with the exception of 6. This sacrifices the manual dark room colours (Interpolated Fading will set itself to ON in the player while this rule is in effect, whether the questmaker actually checked said other rule or not) for the ability to manipulate every questmaker-editable CSet (0-11) on a per-map basis. The GUI in the Map Palette Editor also changes to reflect this, with the numbers now reading 0-11 on the left if they detect that the rule is on and staying as they are if the rule is off. Rows 6, 12, 13, 14, and 15 on the palette now either serve no purpose (unused despite colour data being able to be stored in them), or can be retained for palette cycling should the questmaker choose to use them for said purpose.
I also wonder if a secondary rule can be made that allows for 6 to be affected by the Map Palettes as well for 15 extra per-map/8-bit mode colours, with the understanding to the questmaker that this BREAKS both the default Armor Ring colour-change system and the "Link Colour-Cycles while hurt" setting, and all item-dependent colour changes to Link of this ilk will have to be done using 8-bit Link Tile Modifiers set on the Armor Ring items themselves.