Reading your post again, I understand a little more of your concern. You think there's inconsistency between Qui-Gon's role as a dead jedi in the PT and Obi-Wan's role as a dead jedi in the OT.
As I say, I don't see any inconsistency in the OT -- they don't explain it, but it's clear that Obi-Wan and Yoda know a "trick". Episode III suggests Qui Gon learns this trick on the other side and communicates it somehow to Yoda. This seems consistent. He did not perform the "trick" when he died, so his ability to reach Yoda is a surprise and it's played as such.
If you add Qui-Gon throughout Ep I, II, and III as a voice offering advice and such, you'll be creating more questions than you answer for me.
Before you go any farther, I would ask a few questions: What advice from Qui Gon would make Ep II better? Would he help Obi-Wan's hunt for clones? Would he help Annakin's search for his mother, or his effort to save Obi Wan? He'd probably say "Don't kiss that girl!" "Don't kill those Sandpeople!"
In the OT, Qui Gon has even less of a relevent role to play. To whom would he offer advice? What possible use could it be? Remember he's been dead at that time for about 50 years.