This whole set of pro-PDF responses seem to be neglecting a very fundamental fact. Paper based information is meant for comsumption by humans. Digital information is meant (primarily) for consumption by computers. Sure humans read ebooks, but computers read them a lot more.
Given that, a format that maximizes ease of use for computers is the format of the future. Advanced typography (which is a way to make things more readable for humans, at the expense of readability for computers) will fall by the roadside.
Readability for computers means representing content independently of markup in a semantic fashion. PDF is absolutely (and understandably) miserable at that. So bye-bye PDF and bye-bye advanced typography.