I think I agree with this sentiment. I'm really tired of the prototyping tools oriented around making ridiculous little micro interactions with just the amount of bounce or spring.
That should be built by understanding spring physics and going and sitting next to your implementing engineer. The hard stuff to prototype is what I think you're alluding to, larger navigational or IA types of hypothesis testing.
I also haven't found much there...
e.g. I haven't seen a rapid prototyping tool yet that bridges the gap between powerpoint and coding well. (I hadn't actually found Axure yet, but it looks promising)