Many months ago I installed V3 and almost immediately removed it form my laptop due to the auto-save feature. Just the other day I thought I'd visit Balsamiq and see if anything was done about this, and got excited to see this new optional auto-save feature. Yesterday I installed the current V3.x and today removed it again.
Why? Because although I can enable/disable the auto-save, it's for the ENTIRE PROJECT! Not for individual mockups. So, in the past I could work on numerous mockups and then occasionally save certain ones where I wanted the changes, but not others where I don't. I simply don't realize why this is such a hard concept to understand and why Balsamiq doesn't provide basic Save functionality (almost) any/every other app I've used for 30+ years provides, and even Balsamiq used to provide. Yes, I see the benefit to Projects and wish I could use it. But I simply refuse to be forced into an all-or-nothing save mode.
I guess I'll check back in a year to again see if anything has improved on this. I really like Balsamiq and obviously won't switch (as long as I can keep using my old V2.x).