It's an Adobe product. So you should revert to the standard save, save-as, save-scene-as options. A continuous autosave is confusing for people who want to make multiple versions of their puppet, and it sometimes creates problems and frustration. For example: Finished rigging my puppet. But one thing wasn't working that used to work. So I zipped back in the history panel to find what step it was that broke it. Found it. Oops... made one tiny change, but now my undo-redo history is cleared. Gotta start all over again.
Also, hopefully someday you can link a puppet's performance directly into Premiere or After Effects so you can tweak a performance in CH, save it, and it updates in AE. (Just like your Photoshop changes automatically update into CH). But if you have auto-save, it'll be updating every time you experiment or re-rig for another pose/scene.
P.S. I love the messages autosave gives you after a dozen CTRL+S's.