the PCE has 16 said palette slots for sprites and the MD only has 2...well...that's another headache altogether.
Nodtveidt you hit the nail on the head - right there! Atleast for me anyway. Working with 4 palettes of 16 colors is one thing, but only 2 16color palettes accessible for sprites - that really sucks.
The MegaDrive has few nicities that help make up for it though - 2 background layers (only 64k vram though), sprites as small as 8x8 (good for shooters) and as large as 32x32 with 80 on screen, wider sprites per scanline limit (20), mid scanline palette changes(wish PCE had this), mid frame sprite table changing, mid scanline BG position changing, and 64k system ram.
MegaDrive original games look good and hide the limitations of the system, but certain ports tend not to be as forgiving.
it is SAD that Sega only gave the MegaDrive ~ Genesis the ability to put 64 colors on screen, when the arcade hardware it was sort of derived from (not directly based on), can put 4096 colors on screen.
Considering the competition at the time and the current capabilities of the system, the Megadrive and PCE both were pretty advanced. I don't think they planned on either system lasting as long as they did - well atleast in NEC's case.