Spoilers for the lockpick museum, obviously.
First of all, I would consider sprite masking or shaders to fix many graphics issues. I dont know how I would fix the undo problem described in the Action Keys, though.
Also, the "fundamental colors" I will be referencing throughout will refer to: Orange for Doors, Purple for Keys, and Green for locks. Also dark gray for salvages, and clear for other things (such as sigils).
Action keys will come in all the fundamental colors, though the green and dark gray will have to be repurposed, for things such as jumping or master keys.
Virus keys (or swarm keys) would look like the old virus aesthetic, which would be like red and green mixels i guess.
Void keys would be a sort of anti-glitch key, where if you modify your void key amount for any reason, every other door and key will "mimic" the void color. This might be too similar to Brown/Virus keys, but has a few key differences. It might even be able to open pure doors.
I don't think ghost keys would be an "every other" type thing, instead having a fundamental color associated with them and only intangible-ing when the last action is of the associated color.
Gray keys, instead of making the door negative, will invert the door's effect. This is different in a few key ways, such as dividing when there's more than 2 blast locks, instead of multiplying. Imaginary gray keys, if it isn't too difficult to implement, would integrate or derive the door's effect. These are both surprisingly easy for a computer to do, though they might be a bit clunky in the context of a silly little puzzle game, and I don't have a good idea of how they would look.
When I wanted to make a game with all these ideas, I would have implemented lockets as "amethyst locks": which regenerate the last key collected. This is because, similar to Master Keys, they would seem strictly beneficial to normal contexts. Another idea I now have is carryable doors: which you can carry around. Maybe there would even be a "meta-door", which looks a little like the deltarune chapter 2 hole you put the basket in.
Instead of operation keys, I would implement loggy and expy keys, which take e^ number of keys or the ln of the keys. These, in addition to bicolored blast doors, would allow for every operation.
The reason Omega Keys wouldn't work is because the key amounts are a naturally Cardinal concept, so they would need Cardinal infinities, which is a bummer, since they aren't nearly as interesting. However, there's nothing stopping us from making door amounts be ordinal infinities. We could even use the matchstick representation for the opening animation of the door, with the reassembling getting faster and faster until it approaches a singularity. This raises the problem that not all ordinal infinities are countable, but I doubt this can't just be overlooked. Also, we could instead use Natural operations for combo locks, if we still wanted the key counts to be ordinals.
I don't have many ideas for Star Doors, though I think it would be more cohesive to the game if it was a star lock instead, that a door would have on it. Maybe it could only be opened if the corresponding key amount has a star?
Going with the glass door theming, we could make Nothing doors have a teal-ish outline, like real glass. I would have said every door color would need a corresponding key color due to Glitch keys, but... Nothing doors don't have to have an effect on glitch keys.
Rainbow doors could also be split into two different mechanics: one being named Normal doors, and being themed after the "normal" value in 3d graphics. It's hard to describe how I think these would work concisely, but I think normal base-color doors would act like real-world doors, where every lock would only effect the corresponding key type. Maybe grabbing a normal door would also effect the counts of glitch keys, rather than the colors.
I personally don't find the color groups thing intuitive. But i posted a thing in another topic about "delta keys", which is a bit similar.
I had a cool idea for fractional doors, where you would be put into "fractal time" and do fractional actions. The behavior for this would be unpredictable, though, so I would go against it. Another possibility is that since we already established that our version of ordinals includes negatives, we can simply raise a finite ordinal (or real number) to a negative power to achieve a fraction, and then work from there. This would require storing the numbers in terms of operations instead of literal values, but it would work. Also, fractional doors might only be active from certain sides. I think this is a cool idea.
The idea I had for my game, which is somewhat similar to Entangled doors, is to have multi-sided doors, which have different costs/effects for each side. This would not be easy to visualize in 2d, but I planned on making later versions of my game in 3d, which solves this. Also, it would give us a reason to have non-square doors, since they would have more than 4 sides.
I had multiple ideas for how paintballs could work. Maybe it keeps track of which order you collect paintballs in, and "pops" the last paintball. That would be a cool mechanic. Another way to do this is to actively click on the key color you want to use, though I dont think this is cohesive with the game, especially considering we'd probably need controller support. They also would have a fundamental color, which controls which thing it effects.
Sigils would have a fundamental color, too. Since most sigils would have a count, we could also have sigils for sigils, which would be a neat mechanic for more puzzles. I even had an idea where "0-count" sigils could correspond to "type-shifting" the effected things. (Toggling keys between exact and normal, making locks into blast locks, something else for doors?) Sigils would come in 2 types, multiplier and adder sigils. x1 sigils could force a master key or do the Jammer Sigil thing. There was also an idea for crafting all the doors using sigils, which would go well with the song "Hot Demon Man" (not what it sounds like) from Escaped Chasm.
Maybe pop tiles could be implemented in inverse doors. They would act somewhat like pop tiles, but would also have a cost to "pop". They could also be the +0 counterpart to normal doors.
My idea for omega puzzles would be some combination of Master and Stone colors, maybe called "Limestone Keys". They would be local to each world, and the omega puzzles would be ones where you go into each puzzle within a world and collect newly added limestone keys to use in the omega puzzle. Also, the rest of my ideas open up way too many mechanics to be used in the normal game, so maybe they could be in the Omega Puzzles instead.
I had an idea for "self salvages", which would be both an input and an output. Meta salvages would be cool too.
Thanks for your consideration, or something. It would take a while to read all of these.