IIRC, Alec Guinness shot all his Empire scenes in a day. I doubt Nesson would have had to put in much more work as a Force spook.
What would he have done in AOTC anyway? Scold Anakin for killing sandpeople? And if Vader knew Jedi could come back like that, it would be yet another plot hole anyway?
The ending of ROTS is weaker for lack of Qui Gon. Mentioning him without showing him doesn't cut it, George! ;)