Reason is "Game state is hard".

If you want to save, you gotta be able to take the current state of everything and serialize it, then read what you've serialized and put it back. If you only do checkpoints, you can make assumptions about game state and serialize less.

Generally, it is much easier to develop AI and such when you never have to pull it's state out and then restore it, because if that is done improperly you get bugs like the bandits in STALKER forgetting they were chasing you after a quicksave-quickload because their state machine is reset.

With checkpoints, you can usually say "right, enemies before here? Dead or dealt with. Enemies after here? they're in their default state. Player is at this position in space. Just write down the stats and ignore the rest."

And autosaves just make it one less menu to fiddle with.