2) Qui-Gon clearly had a rebellious streak against the council evidenced in Ep1, but he always followed their orders faithfully, and to the letter. He even died on duty, battling the Dark Side.
3) He DISCOVERED Anakin, the Chosen One, made Anakin's training his dying wish, and correctly foresaw that the little boy would bring "balance" to the force. [Albeit after much carnage.]
4) I really should get a life.
It was somewhat answered in AOTC, though not as well as people would have liked.
basic answer... Obi-Wan and Yoda were decidedly Jedi's of the light side of the force...while Qui-Gon is questionable, (note Count Dooku's comment to Obi Wan when they were chatting about the seperatist movement. Obi Wan says that Qui-Gon would never have joined Dooku. Doku's comment: "Don't be so sure about that. Your former master and my former apprentice didn't always agree with the council."
So you have kind of a gray area in there...and because of Anakin's repentence after the battle between Luke and Vader and the emperor, you kind of sense that there is also a bit of a gray area in him as well...
Yoda and Obi-Wan disappeared upon death. The difference between them and all other Jedi's mentioned who did not disappear upon death is that Yoda and Obi-Wan were Jedi Masters of the Light Side of the Force. I suspect you will see Mace Windu do the same thing when he bites it in Episode III.
Don't put too much into the Count Dooku/Darth Tyrannus stuff about Qui-Gon. Number one, Dooku/Tyrannus was trying to convince Obi-Wan to join with him - he was lying to Obi-Wan (he mentioned that a Sith Lord was controlling the Republic, but he conveniently/deceptively left out the part about him being in league with that Sith Lord). And, number two, we saw how Qui-Gon didn't always agree with the Jedi Council on some thing - like Anakin's training. I'm sure there are other examples in the back stories found in the novels. Obi-Wan hints at some of Qui-Gon's sometimes roguish nature in Rogue Planet which takes place between Episodes I and II.
Also, Anakin/Vader did not disappear upon death. Luke carried out a funeral rite of burning on Endor and later we saw Anakin's spirit appear next to Yoda and Obi-Wan. There is a bit of contradiction there, but it possibly has to do with the fact that Anakin/Vader was, right up until his death, heavily into the Dark Side of the Force.
Of course, this is just us Star Wars fans trying to draw lines between the continuity stretches, bends and breaks that Lucas and his corporate entities have caused.
But, wouldn't that requre believing that the Count had a shred of honesty?
The dark side loves to lie, you know?