If there was a way to manually remap palette entries directly from the palette box in pro motion, I'd use that program all the time. The plugin which allows palette remapping is so slow an cluttered compared to, say, mtPaint's built in feature where you can just drag and drop entries within the palette window itself (which, by the sound of it is the same as in GG). I also don't like how in promotion, when you cycle through palette entries you are able to accidentally cycle past the entries you want to use because it doesn't let you set a limit (which mtPaint does).
(btw mtPaint sort of sucks for animation so I don''t mean to mention it for heyy13's original topic of animation)