Qui Gon was actually as far as i know in the shooting script for Episode 3 where he teaches Yoda the concept of joining with the force, and talks about the Whills. It is in the novelization.

Lucas apparently discarded the scene because the information or scene was not important in the final cut of the film, Or they just will not say that Liam Neeson turned it down just like Sean Connery turned down Crystal Skull.

Supposedly working for Lucas is poisen for your career as an actor as you get either typecasted or remembered for being in a childish video game movie.