It has to do with the nature of a multi-level explorable world vs a linear mutli-level game. In a typical LT2 game -- or most FPS and many RPG games -- the player goes through a chain of missions. Once a level is completed it isn't used again. If it is used again then everything respawns either exactly as it was initially or it sets up a new scenario. But levels in an M&M RPG need to remember their states between exit and re-entry. This is what the mini-saves do. When you enter a level and the games does not find a corresponding mini-save then it spawns the level in its initial state. This can fact be abused, but removing mini-saves has been the only solution to many folks' problems with MM9.
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