My problem with the Brian Herbert novels was Kevin J. Anderson, who I have always regarded as the hackiest of hacks, though I suppose he has some serious competition now from Scalzi... at least Anderson actually does have story ideas, he just sucks at delivering them.
Curiously, many many moons ago I read a book from Brian Herbert that was, to my adolescent self, quite enjoyable, so I'm certain he could have handled the writing chores himself. Perhaps hiring a hack to do the typing was an easier way to milk notes than doing it himself?
Aside from the Hack Author problem, I do feel a LOT of what is wrong about the prequels is that sometimes a good writer comes up with a consistent back-story to support his setting, but recognizes that its half baked and, well, bad. Good enough for back-story, but awful for... you know... story. The Prequels of Dune pretty much fit that to a T, if we assume that Brian and Kevin didn't actually make up most of the details. Too many coincidences, too few highly important characters doing all the heavy lifting for humanity with a population in trillions, and over too long a span of time. How miraculous that Spice is discovered at the same time as the Butlerian Jihad is winding down, and that so and so was the daughter of the leader of the Witches who would found the Bene Gesserit AND was herself the secret mastermind behind the Holtzman Generator... which, ALSO, was developed at the same time the Butlerian Jihad was winding down... which ALSO happened to be the same time the Bene Tlielax were being founded, by someone who helped discover spice AND had a relationship with the Witches of...
Are we sure the universe of Dune isn't a sleepy little seaside village in northern Maine, with a population of roughly twenty people?