Qui-Gon and his Ghost Powers?
 

What does the book/deleted scenes etc tell us about it that the movie doesn't?

In AOTC - Qui-Gon does have one line. Yoda hears him at the same time he senses when Anakin kills the sandpeople.

So, the films do set up that Yoda will be able to/does talk with Qui-Gon.

Didn't Yoda say in ROTS that he can communicate with Qui-Gon and that he will teach Obi-Wan how to as well?

this scene didn't make any sense (to me), it felt like a complete throwaway line and plot diversion.

I'm guessing Lucas wanted there to be more to it, but couldn't get Neeson.

I thought that there was a Neeson scene filmed, but it was cut.

I'm confused too. I remember hearing that Neeson had signed on for all three films. Not major roles in each, but at at least some type of cameo.

If it was filmed, hopefully its put in on the DVD.

I thought I read somewhere he wasn't in ep2 due to breaking his leg
but who knows

I thought it was put in there specifically to explain why Obi-Wan was able to talk to Luke in the original trilogy. He learned this from Yoda. But when it appears as a one-liner, it seems a little forced to me. Like Padme saying "Luke" and "Leia". Yeah, I get it, but why would she be throwing out names while giving birth?