Greek philosophers vs. German philosophers
Actually, I would prefer the Western world of philosophy against the Eastern world.
This would contain loads of Socrates versus Confuscious action right there. I would perfect the art of using Nietszche's most likely Yoshimitsu/Voldo fighting style to kick Aristotle's ass, use Socrates simplistic yet badass, obviously SUPER SAIYAN-LIKE power to destroy a majority of the Pre-Socratics while tag-teaming with Gaunilo to tear apart Mr. Saint Anselm. This is a game I would play. Like making your own single match 'quick fight's in most fighting games and choosing the character that most annoys you so that you may tear it apart would become a mainstay of this game that would keep me coming back to it for a long time.
I also promote the Hellboy/B.P.R.D. Vs. The League of Extraordinary Gentlemen idea, which is excellent and should be done but might never be done because the characters would be a bitty limited. I mean, we're only using the heroes here. So instead I propose a game along the lines of Ultimate Jump Superstars (A DS game of many, many anime characters.). This game would instead utilize the either independent (more independent than most), or lesser known comic books industry characters in a free-for-all fighting game. I would love to see Cassidy of Preacher in a fight with the Sandman, or Atomic Robo against Hellboy, or even Rorschach against Fone Bone (What.). As Yahtzee would say, a fan-fiction/huge circle-jerk.
As a last request, throw the entire pantheon of Old Ones in one of these games as either a plot, environmental hazards, specials, or 'help' characters, but do not let me play as them.
EDIT: Got rid of the phrase "fanboy fan-fiction" for being blatantly redundant.