I always thought that Psycho Mantis boss fight was cool how you had to change controller to a different port for the fight. I also liked how his dialog changes if you have other Konami games saved on your memory card and depending how many times you saved he would have different dialog.
What are some of your favorite game mechanic? What are ones you would like to see be in games?
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An experience system, like the one in the PS1 game called Shadow Tower, where you don't allocate your experience points, but instead how you do in combat governs your stats, like getting hit will potentially start increasing your health and defenses, attacking with a certain weapon type increases the damage output you deal with the weapon type, and so forth.