in addition to the things mentioned above:
1) Real camera and 3d placing of the layers. I am not talking about obj or any kind of 3d mesh support, no, just a 3d world to place assets around, like in Toon Boom, or HitFilm software.
2) Per Layer and per Sprite masking options. The current webGL (?) Destination Over,Out and whatever, are hard to implement and have a counterproductive workflow. A system that uses either gray-scale maps, or opacity values to mask any number of layers or objects (using other layers and/or other Sprites) will be ideal.
3) A timeline on the editor, with key-frame capability, to visually time and move objects around, add/or trigger events. This...
4)...in combination with a curve-path editor for making paths ( attach object to a path, set speed, way-points, ping-pong behaviors etc).
5) A multichannel sound mixer/system. Play multiple sounds at the same time (not with 16ms delay), balance the volume/pan output (without 3d sound) for each one, or any combination of them with buses (groups), behaviors for easy in/out fades.
6) Affect particles after their creation with events.
7) Official implementation of R0J0Hound's Canvas plugin, with tutorials suggesting practical examples and how to make them.
8) Although RookieDev mentions it, I also must write it down my self: Real-time light-shadow system. It will just blow away the visual quality of our creations, and add a ton of new aesthetic and game-play possibilities!!!