I definitely agree with you that this film's content especially in the first half hour or so, but at the end too, is rough to watch for many people; it was even for me. If Gordon-Levitt gets recognition for this or not, he will probably do well over time. He is one of those actors willing to take risks and explore new territory and sooner or later that will pay off for him in solid respect for his work as an actor. About the movie's sci-fi content, I can only repeat to you that though I didn't read the book, this is the essential element in it.

[* * * * *WARNING: POSSIBLE SPOILERS* * * * *]

I think the two characters allow the book -- and the movie -- to explore two contrasting responses to the trauma of being sexually abused. One is to embrace it wholeheartedly and seek a life of dangerous sex; the other is to black out and shut down and wander through life in a daze. The experience of exploring what really happened to him is Brian's way of slowly coming to terms with the trauma. The alternation between the two lives is the way the story is put together. I think it's quite valid. Personally I find the idea of alien abduction is pretty hokey too, it's not anything that personally appeals to me very much, but in the screenplay, it works pretty well.