My understanding with the whole Liam Neeson thing is this:
For Attack of the Clones, George Lucas didn't ask him, he just recycled audio from EP1 for the scene where Yoda is meditating and hears Qui-Gon pleading with Anakin to stop slaughtering the Tusken Raiders.
Supposedly, the re-use of his voice did not sit well with Liam and he complained to George. George responded with the fact that when Liam signed his contract all rights to to Liam in the likeness of Qui-Gon were owned by Lucasfilm and that includes Liam saying Qui-Gon dialog.
I'm not sure what the outcome was on that, but when it came time to put together ROTS, Liam Neeson basically told Lucas to go-to-hell since he didn't want to anything more to do with Star Wars.
Also, it really depends on what interview you see with Neeson. In early interviews around the time the movie was being promoted, he's very positive. In later interviews, both he and Ewan complained about all of the green-screen work and how acting was secondary to interacting with the visual effects - and as such they didn't enjoy Star Wars as much as they had hoped they would.
Perhaps these are just rumors, but having Qui-Gon appear near the end of ROTS would have made the movie (in my mind) PERFECT.
Lucas even kept promising that in ROTS we would learn the secret of how Jedi can appear as force ghosts after death.
A scene with Qui-Gon speaking to both Yoda and Obi-Wan would have been awesome. What we got instead - an imaginary conversation in Yoda's head - was just lame.
It's one of those things when Lucas should have paid Liam Neeson whatever he wanted just for dressing up as Qui-Gon one more time and saying three or four lines - for the sake of making the PT all that much better.