Road pedal systems have bigger platforms and more sophisticated float systems.
MTB pedal systems allow for MTB shoes (easy walking), mud shedding, and quick entry to the pedals being that there is lots of on-again/off-again in MTB racing. Quality MTB pedal systems feel primitive compared to the quality road system.
In short: If you ride long, go with road. If you are on and off the bike (like bike messengers) then go with MTB. This, btw, is why messengers who did ride clipless, preferred MTB systems.