If you actually intend to keep save points, you can rename them in your save folder to something more descriptive. It has been a while but it seems to me that I did this with a couple saves a few years ago. Mainly kept as save points in case of beta bugs cropping up and need to go back to an earlier point.
I'm sure this wouldn't be possible in multiplayer, but should still be fine in single player saves. A "Rename" option in the save file GUI would be a nice addition, and should not be too difficult to do. Adding a comment to the file that shows up in the GUI would be harder, but yeah that would be nice also.