I can't think of any missing feature right now, but if it helps, my current workflow is the following:
- Open a high resolution input image with Gimp to add an alpha channel, remove the background, improve the edges of the target shape, etc.
- Let PixelOver do its job with the image :) . As I said, I usually only use old features.
- Do some final touches with an image editor like Aseprite.
Thinking about it, maybe an interactive background remover would be nice :)