Theres a program called azdrawing it's japanese and it's free, It has some nice features that perhaps you could take inspiration from
It uses the layers as animation frames and it has a neat function for filling everything under a lasso selection
I translated and customized it for frame by frame animation
For quick playblast you can press F9 (linetest) after you've activated animation mode (N)
I've uploaded the version I worked on this link in case you guys want to try it out.
http://cgmodelers.com/yourls/f3
To ennumerate useful features
It has a proprietary format .azw however it uses also psd
- The timeline is the layer order
It has a penciltest function wich you can trigger with F9 after you've animated some frames
Animation Mode (Triggered pressing N)
Multiple reference layers
I hope you guys can take a look at it