I've never liked relying on auto-saves, it seems I'm the only one among my friends who don't use quick-save keys when playing on PC, I like setting up around 3 saves so I can go back to different parts if I'd screw something up, though I rarely have to load up anything but the latest save.
As for worst save system, I think I'd go with Morrowind or Black, Morrowind for technical reasons, because it's auto-save feature was buggy and seemed to introduce minor errors every time it saved, which would after some time accumulate into a corrupted save file, and the same thing occured on your regular saves too, but there you could at least fix it by manually making a new save every time you saved.
I'm sure Black isn't an exception when it comes to console FPSes, but it's the one where the save system has been bugging me the most. It only saves between missions, and missions can get very long at times. There are checkpoints within the missions, but they are only used if you die, if you have to do something and exit the game all progress in the mission is lost, that has resulted in me being stuck in a mission for about a year, since I rarely have time to play it more than about 40 minutes straight, and the mission is longer than that, at least if you die occassionally, and as I can't finish it, I have to start it over every time.
Because I don't rely on auto-saves I've never had any issues with System Shock 2, except for co-op, since you have to be the same number of players, the exact same players and connect to the host in the same order for the game not to crash when you load up a co-op save game. That didn't stop me and a couple of friends from playing through the game in co-op several times though.
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