The more I watch this show the less I like it. With Qui Gonn showing up as a ghost here it completely ruins the end of ROTS. Why was Obi-Wan surprised to hear Qui Gonn is able to communicate with the living when he's already talked with him?!
For that matter, why is Qui Gonn asking questions about how Anakin was trained? We're supposed to believe he's been watching all along since he tried to stop him from killing the Sandpeople in AOTC.
1) Because his experience on Mortis was so far outside the realm of human experience that Obi-Wan probably suspected it was a dream, or an apparition, or manifestation of his subconscious. We don't really even know yet if that really WAS Qui-Gonn. We know the Son was impersonating Shmi, and it's a safe assumption that the Daughter was impersonating future-Ahsoka. Maybe the Qui-Gonn vision was the work of the Father, trying to glean more clues about the path of the Chosen One.
2) As far as the line of questions, again, not sure that was really Qui-Gonn. It could have been the Father or possibly even one of the siblings trying to find out more information about Anakin. Or maybe it WAS Qui-Gonn, and he just wanted to hear Obi-Wan's assessment of the training to this point. Or more to the point, he wanted to hear his "point of view" because so many of the truths we cling to depend on our POV, yadda yadda yadda.
I really think the brilliance of an episode like this is that it does lend itself to interpretation and allows enough wiggle room to satisfactorily explain away most of the weirder elements. (Like where is the sunlight coming from?) I also think it opens up some really interesting questions about the Force itself, and the fact that the Sith and Jedi are just practitioners, and not really the end all be all of the various paths.