It would be great to have some way to have a drawing software and Spine sharing the same format with layers.
I feel like there is also a room for a whole new software especially made for game asset creation supporting stuff like quick test posing, easy scrubbing through drawing substitutions and frame by frame animations, automatic conversion to different resolution, trimmed export and of course seamless export to spine. Naturally this thing would need good painting tools which are probably very difficult to program, but I am just saying... feel like this doesn't exist and could be used in a lot of game studios.
If you have a character with a lot of drawing substitutions I can only recommend using an animation software if you happen to have one (e.g. ToonBoom Animate Pro). This way you can directly test the frame by frame parts and scrub around in the timeline to see all the possible substitutions. Often these programs have possibilities to export all layers separately as an image sequence already build in. Together with a script to kill duplicated images and Photoshop to trim this workflow works great for the project I am currently working on.