Also, maybe disable the layer mouseover highlighting feature during playback? I find it useful when selecting, but distracting while previewing my animation.
Some improvements to speed up Z-order sorting - moving multiple sprites simultaneously, keyboard shortcuts to move up/down one layer or move to top/bottom (like ctrl+] and ctrl+[ in photoshop), and definitely something along the lines of copy&paste just z-order to all frames.
Filtering both z-order and animation layers by name could be extremely useful as well - the project I'm working on has 52 sprites for the main character and it's sometimes cumbersome to look for the appropriate one.
Lastly, not sure if already mentioned elsewhere but it would be nice if the timeline could automatically delete "empty" keyframe markers at the top when there are no keyframes remaining on any individual layers at that point in time.
Sorry for spamming your forum with a bunch of suggestions, my wife and I have really been enjoying using Spriter so far and it's opened up a lot of possibilities for the C2 project we've started!