I was going to create a new thread but I think I may as well just continue here.
I saw Filoni said something the other day about the 3 way dual at the end of TPM. Basically saying there is an extra weight to it because Qui Gon was the only Jedi who could have properly trained Anakin. Now for certain the fact that Qui Gon isn't in perfect lock step with the Jedi is present in the movie but to make the jump that he was the only Jedi, and he knew he was the only one he could, you have to make a pretty big assumption on your own part.
Ofcourse I think this is a pretty cool idea and kinda wish it would have been more obvious in the movie. You could do it without really even adding a scene, just change one or two existing scenes. Instead of the Council refusing Anakin's training have them be like "oh yeah this kid is the Chosen One, thanks for bringing him to us. We got it" and then Qui Gon refuse, insisting he train Anakin himself. Then later have one scene where he and Obi Wan talk and Qui Gon explains the flaws in the Jedi thinking that he knows would fail Anakin and how he, and he alone, can train him correctly. You could possibly take it one step further with Sidious maybe even mentioning to Maul that Qui Gon must be killed.
I think this plays into the whole shades of gray idea. I mean if the Jedi are inherently good and good intentioned but their flaws lead directly to failing the Chosen One and having him become evil that is a shade of gray right there.
Also going forward into the PT the fact that Dooku was Qui Gon's master could have played into this idea. Have Dooku say to Obi Wan "hey Qui Gon knew the Jedi were messed up, I knew too. Eventually it got the point I had to leave." This is somewhat hinted at but is far from front and center.
Even as a PT fan the fact that this idea that Qui Gon's death is so momentuous and that had he lived Anakin's fall would have been prevented is kinda not really put out there is frustrating. Many fans, including me, have issues that Anakin is a child, that Qui Gon takes time away from Obi Wan would have been alleviated by this. Qui Gons role and importance would have been more obvious.
According to Filoni these are ideas Lucas had when making the PT, why didn't he actually, ya know put it in the movie?