Just saw this. As a big X-Files fan, I digged it.
I can see now why this flopped. It was a very personal movie to Carter, Mulder, Scully and the fans. You could just tell that Carter wanted to tell the Mulder/Scully relationship story to the end. A very ballsy move from Fox to approve this. Basically IWtB was a drama movie, the thriller aspect was just the secondary plot. Personally, mainly the only thing I didn't care about this "episode" was the Scully/doctor/hospital/sick kid -plot. It was necessary for the behaviour of Scully, but we less of it wouldn't have hurted anyone.
And I really liked the end credits scene. Very nice "Goodbye, everyone!" thingie.
(If this really was the end...?)