One thing I wondered is what Fischer was supposed to remember from his dream. My best guess is that he was only supposed to remember the very end, the moment with his father, since it came right before he woke up. If he remembered the whole thing, it seems like the idea they wanted to implant would have gotten lost in such a complicated story.
The only thing is, didn't everybody spend a while climbing out of the van and sitting on the river bank waiting for the dream to end? Why wouldn't he remember that instead?
I'm also still confused about why they blew up the base/hospital in the third dream level. I thought they couldn't get out of a dream by dying.