The long and short of it is this: the two games may be graphically coherent, but because they were released separately, it's logical to keep them separate, and in doing so helps with keeping the content organised as you can see it. I'm guessing you've not seen the Flash Cycle palettes on my current sheets for Mushroom Hill, Lava Reef, Sky Sanctuary, Doomsday and Mecha Sonic? And just because there's no underwater over in Sonic & Knuckles, doesn't mean 'there's less palettes'. Same applies to his Super form and his Hyper form. The general palette used in Sonic 3 and Sonic & Knuckles are one and the same. There's no such thing as 'Sonic (S&K Palette)'.