I was messing around with Mega Man Wily Wars on different emulators. The one with the most accurate color palette on games seems to be Megasis. Unfortunately that emulator hasn't been updated in years. The problem with this emulator is in some areas in MegaMan Wily Wars, the stages have glitch like backgrounds.
Other more updated genesis emulators have these errors corrected. Unfortunately, the colors are incorrect. They are either brighter, or darker than Megasis, though mostly brighter. I'm trying to find one that displays the genesis games in correct palette colors like Megasis, but is more updated than Megasis.
I have tried Kega Fusion, Gens, Regens, Ages. A lot of them similar, though don't have a correct palette. Not to mention none of the genesis emulators have a palette editor for this kind of stuff.
Also, I haven't touched genecyst in years, since that one was a DOS emulator of their time. I doubt it could run on DosBox though.
But yea. Megasis is the only gens emulator that I can find that seems to have the correct color ratio. Just that it has some random background glitches, especially on some stages on MegaMan Wily Wars.
Also, I don't have any recent save states of MegaMan Wily Wars where all 3 Mega Man tiles start at Wily stages. All the ones I had were from some DOS genesis emulators.