January 20 update:
Read 5 pages of 時をかける少女 today – presumably, chapter 13. I think I have an idea where the story is heading. I felt this way for a couple days now, and each new chapter strengthened my suspicions. I’m also kind of excited that I can make some predictions (even if I end up being wrong), because when starting this book, I wasn’t even sure I’d be able to follow the story to a reasonable degree. Expectations subverted! 
Oh, I felt exactly the same way! I couldn’t parse a lot of the details, but it sure seemed a bit too much.