Looking back on it now, I think the one thing that's really not plausible is the idea that someone could write a system that can anticipate anything that can happen. It was a little too Foundation/Psychohistory for me.
But it was still a fantastic novel, I loved reading it, and will probably re-read it again and again.
I did, yup. I was actually super mad at Daemon; I always try to get people to get both at once, to avoid the cliffhanger.
I don't think it address it enough; it made it more plausible by admitting that it can't be completely autonomous, but I'm not entirely sold. Having said that, I still love the series, much like I love any fantasy novel :P
But it was still a fantastic novel, I loved reading it, and will probably re-read it again and again.