I think it would be really neat if in the next MK, there would be different bosses depending on whether or not your character is good or evil. For example, if Shang Tsung was the boss normally, if you go through the game with either someone on Tsung's side, or Shang Tsung himself, your boss would be Raiden. (or whoever the power struggle is between in that particular game).
I've also always thought that if you go through the game with certain characters, they should have certain fights that are mandatory. Like, for whatever fued they have in that particular game's story line. For instance, Kano would have to face Sonya at some point.
Just some idea's that I might like to see in the next game. Let me know what you think!
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TJ