I never though much of Dune 2-5 either, but I guess I'm in the minority on this one.
I think the reason people have trouble with 2-6 is that they're ultimately a reversal or deconstruction of the Hero myth. The first book is a fairly typical "Rise of the Superhuman Hero" tale, and that's why it's accessible. Book 2-6 explore the dark side of this myth, which is why they're unique, somewhat inaccessible, and really interesting.
As regards deconstruction, I think Gene Wolfe does it so much better than Herbert that I don't really consider it a selling point that Herbert tries to do it.