When he first saw the film a close friend was really confused by the Qui-Gon reveal at the end of ROTS. "Wait, huh? Qui-Gon? That was out of left field! Why didn't they show Yoda talking to his spirit then?" I then told him the silent meditation scene was supposed to be Yoda communicating with Qui-Gon via the Force. "Oh, okay. They didn't get that point across very well, then."
I can't say I was entirely in disagreement with him. If you don't know that the silent meditation sequence was connected to Qui-Gon then the later conversation with Obi-Wan can seem like a big HUH? DID I MISS SOMETHING? moment.
I'm fine with it now, but I understand the confusion.