I press ^S to save my project extremely frequently while developing - it's rather a pain that Snap! insists on stopping my project whenever I do that. :'P
Congratulations on the Snap! 5 release, btw!!! 
The trouble is that it's hard to be sure you've chased down all the pointers when things are changing value underneath you. Saving the project is like doing a garbage collection -- you have to see what points to any bit of storage.
There are incremental GC techniques, but they're complicated, and GC is actually easier in that it's no big deal if you forget to reclaim some piece of garbage (and it gets collected in the next GC). So, this is a long way off.