I see what you mean by having Anakin communicating with Qui-Gon throughout the trilogy. Having Anakin being able to hear Qui-Gon would emphasise his power as the chosen one. And I like the idea of Anakin calling out to Qui-Gon at the end of Sith would be an awesome parallel with ESB. For some reason, I was thinking you guys were talking about when Ben appears to Luke on Hoth, instead of when Luke was calling out to Ben on the Cloud City weather vane. Thought would be a great change.
Maybe you should then construt a difference between hearing dead Jedi and seeing dead Jedi. Dead Jedi could talk to those who are able to hear them, but they can only be seen by those who learn how. If you change that one Yoda line, it would set up the scenario nicely.
What happened to Sebastian... uh, Anakin is that he died on the ramp of the shuttle. He didn't show him fading away. The shot cut away before it happened. If it did. Next time we saw him, it was the suit burning on the pyre on Endor. Sure, Anakin could have been in there, but it didn't need to be. Besides, burning an empty suit is a fine symbol of the end of the Empire. THis is the lastshot of Anakin in Jedi:
It is a couple of seconds long. Should it be necessary, It would be easy to edit Anakin fading out here.
-TheSluggo