I'm a big fan of Iain Banks since reading Excession (which still remains my favourite). Also loved Dune, but haven't read any of the sequels yet. I'd also recommend Catherine Asaro's saga of the Skolian Empire to anyone that is into physics/maths.
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.
First, rather than just telling a masterful story with compelling characters, they over-explain and lean heavily on disturbing scenes. For example, in the originals, Gurney Halleck was simply (or not so depending on how you look at it) a very loyal and honorable person..it was that simple and beautiful. The prequels go out of the way to explain that the loyalty comes from being tortured and having his sister raped by the Harkonnen's. It's like the stupid Midi-chlorians.
Secondly, every book comes off as though they are trying to make you buy all their other books. Forget about reading their "conclusion" to the original series (book 7 and 8) without reading their Legends of Dune series. They go out of their way to make references to their other books, even when it isn't necessary.
Argg...sorry I got upset there.