This thread doesn't compare any hardware issues, only the soft counts, which was released on both systems. here's my rating:
Shooter/3D Shooter:
Air Buster/Aero Blaster – MD>PCE
After Burner II - PCE>MD
Atomic Robo Kid – PCE~MD (different)
Daisenpuu - MD>PCE
Darius II - MD~PCE (different)
Forgotten Worlds - PCE>MD
Heavy Unit - PCE>MD
Hellfire - MD>PCE
Kyuukyoku Tiger (Twin Cobra) - PCE>MD
Raiden - PCE>MD
Tatsujin - PCE>MD
Winds of Thunder/Lords of Thunder - PCE>MCD
Zero Wing - PCE~MD
Adventure:
Snatcher CDROMantic - PCE~MCD
Beat ‘Em Up:
Street Fighter II' Champions Edition - PCE>MD
Fatal Fury 2 - PCE>MD
Fatal Fury Special - PCE>MCD
Art of Fighting - PCE>MD
Action/Jump ‘N Run:
Bonanza Bros – PCE>MD
Cadash - PCE>MD
Chiki Chiki Boys - PCE>MD
Daimakaimura (Ghouls 'N Ghosts) - SGFX>MD
Gain Ground – PCE>MD
Golden Axe - MD>PCE
Juuohki (Altered Beast) - MD>PCE
New Zealand Story - MD>PCE
Ninja Warriors - MCD>PCE
Prince of Persia – MCD>PCE
Rainbow Islands – PCE>MD
Rastan Saga II - PCE~MD (same shitty)
Shadow of the Beast – PCE~MD (Music only: PCE >>>>> MD)
Strider - MD>PCE
Turrican – PCE~MD (same shitty)
Valis III – PCE>MD
Wonder Boy III: Monster Lair - PCE>MD
Wonder Boy in Monster World/Dynastic Hero - PCE>MD
RPG/Action-Adventure/Strategie:
Dragon Slayer: The Legend of Heroes – MD>PCE
Dragon Slayer: The Legend of Heroes II – MD>PCE
Dungeon Explorer – MCD>PCE
Exile – PCE>MD
Langrisser – PCE~MD
Popful Mail – MCD>PCE
Populous – PCE>MD
Shin Megami Tensei – MCD>PCE
Sorcerian – PCE>MD
Ys III – MD>PCE
Geschicklichkeit/Puzzle:
Bomberman '94/Mega Bomberman - PCE>MD
Columns – PCE>MD
Devil Crush – MD>PCE
Lemmings – PCE>MD
Puyo Puyo – MD>PCE
Puyo Puyo Tsuu – MD>PCE
Volfied - MD>PCE
Sport/Racing:
Dodge Danpei – PCE>MD
Hit The Ice – MD>PCE
Outrun – PCE>MD
result:
PCE: 28
MD: 19
Draw: 8
any other games to compare are welcome (if there're some others)

also everybodys own rating would be interessing
