Well I remember distinctly, it was no secret how much he hated the green screen process and Lucas' emotionally-void directing. Neeson hated it, and actually stated that he was so disillusioned with acting he might retire. Seriously. It took him a while to calm down, but he was still done with it.
And I don't think anyone believes Qui Gon wasn't supposed to cameo in Episode II or III. In fact, he was supposed to appear in Episode II in a cameo, and then wasn't the press statement that he'd had a motorcycle accident or something? Funny that in 18 months of post production, when they did a month of reshoots AND green-screened in other actors like Oliver Ford Davies, that Neeson wasn't available for his ONE SCENE. And look at the Force ghost explanation that is thrown in at the end of Episode III.