In the matter of Qui-gon, I believe making him disappear would be problematic, as we would be left with the question of why he did dissappear when all the other Jedi that died in Geonosis did not. In the Episode II novel Yoda is surprised when he is in meditation while Anakin is killing the Tuskens and he hears Qui-Gon's voice, he is surprised because up until that point no Jedi was able to retain his identity after becoming one with the force. This is the technique that Yoda will learn from Qui-Gon and pass on to Obi-Wan between Episodes III and IV, I think this is best left alone as seen in the films, it adds a little mistery and if anyone tries to change it it would only become more problematic and confusing.
My opinion is it should be left alone, we know enough, before Qui-Gon all Jedi would die and become one with the force ala "Nirvana", he somehow found a way to retain his identity and communicate with the living after death, he passed on this knowledge to Yoda and Obi-Wan who perfected this technique and therefore dissapeared after death and were able to communicate with Luke as a voice in ANH and later on as an apparition.