IMO, the skill of the designers has a lot more to do with the way the game turns out than the hardware does. The Genesis may have a very limited set of subpalettes but can easily do things with its video hardware that are real headaches on the PCE. The SNES has the widest range of colors but can't display as many on-screen as the PCE can, though its overall graphics capabilities are beyond both the Genesis and PCE. The PCE buries both in terms of displayable colors as well as free cycles, but that's all for naught if you don't know how to exploit these things, and it seems like so few companies really knew how to work the hardware back in the day. Ultimately, if you were to take one game and develop it concurrently on all three consoles... which would look the best? My money's on either the PCE or the SNES. Which would play the best? Either the PCE or the Genesis version. Which would sound the best? Depends on whether or not you used the CD... the CD gives the Genesis and PCE a distinct advantage over the SNES in this department. Without it though, it's hard to say... just depends on how well you can work their respective sound capabilities.
There is no absolute best between the three, no matter how fanboyish we may get around here. There is always going to be *something* that one of the other consoles can do better with the same game, no matter which one you're defending.