Save Points, I assume that you go to some place and initiate an interaction to save. Auto Save, I assume you mean checkpoints that once you pass it automatically saves your progress.
The advantages of auto saves is that the player doesn't need to worry about saving. If the player dies after completing a big and difficult task, it can be frustrating when you forget to save. The second advantage is you can even place more points than Save points. Thus saving is done far more often than a player would do, because saving also interrupts the gameplay momentum.
The advantage of save points is that often in these systems, the player can choose the save file. That includes creating a new file, making it possible for the player to return to an earlier point and take a different route. The second advantage is that the player can interrupt his quest to do some leveling up or just look around in the world.
Thus, whatever you choose it has good and bad points.
