Ive been using aseprite -
http://www.aseprite.org at home and Sprite Something on the move (app store).
I don't know but I recon if the character can work without grey it may be best due to the memory problems it could cause, especially if they all are animated, or has this issue been fixed?
I too have been toying with the idea of an RPG with a turn based fighting system, but think the biggest obstacle is going to be getting everything on the screen at once without it being cluttered. Only having 4 possible actions like in the gameboy Pokemon as oppose to say final fantasy where you may have 20 different magic attacks is a good move. Maybe also hiding enemy health bars could save space on the screen and add to the mystery of how powerful they are?