I'm not sure how you would go about doing this, but one thing I would LOVE to see is a layer that doesn't change the pixels, but would adjust the position of the pixels. I know that this isn't exactly traditional pixel-art technique, but it would save SO MUCH time.
Example: I have a BIG BOSS. I move his torso every few frames, but I only animate the arms/legs/secondary animation layers. I get to the end of the animation, realize I forgot to add a belt-buckle to the torso. Even though the torso is the same in every frame (position has just been changed) I have to go back and add the buckle to EVERY frame. It would be nice to paint the buckle on one frame and it automatically add it to all the others with updated positions.
You'd probably have to create some sort of special layer, similar to a smart object in Photoshop or a composition in After Effects. Again, this is just a suggestion. I figure it may be a bit advanced. I use puppetting in After Effects a lot, so it's nice to have a layer with transforms that I can go back later and edit the innards.
Thanks for the awesome work!