This has been one of the problems I have had with Lucas. He puts his big thumbs up for all of these EU stories, but can't even bother to integrate them coherently into the prequels. I just find that to be extremely ******, that he'll make all the money off the backs (hands really) of the EU authors, but will totally disavow what they have come up with when it doesn't suit him.
Ok with the rant out of the way, here's how I see the revelation in ROTS working in conjunction with how Jedi spirits work in the EU...
While Yoda indicates Qui-Gon has found a "path to immortality" it doesn't mean he has the ability to communicate with the corporeal world indefinitely. Taking a look at the Marvel comics of the 80's, they had a higher plane of existence where Jedi went to when they died, an aether if you will. Here is where they would "live" for eternity communing with the greater Force, but their connection to the mortal coil is limited only to a certain amount of time. This would be so that they do not effect the physical plane, as they could accidently use the knowledge that they have gained to adversely effect the physical plane. This would either be a self-imposed restriction that the Jedi must place upon themselves, or more likely a restriction by the Force to keep the proper balance between the two planes. That is why Obi-Wan, Yoda, and Anakin only speak to Luke and Leia for only a few years after ROTJ.
Also I don't believe the Qui-Gon is the first to discover the ability to communicate from the netherworld, as EU establishes that Jedi and Sith in the past could do just that. I think he re-discovered the ability, something that was lost to the Jedi over the millenia.
Now as for Anakin Solo, I thought I recalled that at some point in the New Jedi Order, Jacen had a vision that equated to Anakin speaking to him from the beyond. I might be wrong on that, but it has been a while since I read most of the books...