Hello there,
As games will tend to get more advanced with Stencyl's evolution, I think that it would be nice (if not life-saving) to have some kind of version control. Something like Tortoise SVN but simpler.
Maybe just a easier way to make backups of stable versions of the game. Something like a "save as stable version" and a "Revert to version X" on the file Menu.
(Ok, right now you can actually do it just "saving game as" and save with another name, I'm just trying to figure a more advanced and friendly way to do it)