The reason autosaves weren't implemented was due to a few factors:
A) At the time, manual saves were the best way to do a non-permadeath run. Since then, the new difficulty options made going back to an old save relatively pointless, as you can continue playing right after death, moving forwards rather than back.
B) It's extremely hard to track down a specific reason why a save file won't load. The only way I can reasonably get rid of them all is if people report it to me. So it's not as simple as checking to see if the save file is cool or not. This is the same reason why I don't allow cross-version save files (for now).
C) Time cost that could be spent on more enjoyable tasks. Axu is still in Alpha, and being developed in my spare time. I put my effort towards facets that pique my interest at the time rather than what absolutely needs to be done at that time. If I were developing Axu full-time, my priorities would be much different.
The best short-term remedy I can offer is to have some kind of "Save without quitting" option as a last resort. For now, autosaves aren't something I can afford to put time into.