Revned Said: I couldn't come up with an elegant way to show the disappearing blocks in Mega Man 3. The first time I mapped it I just left them out, but then I put them all in the next time. Ideally there would be some way to represent the different groups, but I can't think of anything that would look natural.
I also wish I could find a good way to show palette shifts without leaving glaring seams, but as your Mega Man ending rips showed, it's not very straightforward. I experimented with dithering myself, and it just didn't fit the style.
Are you talking about showing the order in which the temporary blocks appear? Other than making an animation like Revned showed, I guess you could stamp big numbers on each block to show the sequence, though that would look kind of ugly.