Truthfully, "God Emperor of Dune" is the best book in the series, but you have to read the second and third books to get to it. And they are… They are just the worst.
—Dave Kellett
This is completely true. We can theorize about how Chapterhouse: Dune or the final book might've been the best if Frank hadn't been dying, but certainly the abominations perpetrated by Kevin J. Anderson (worst writer in the world) and Frank's incompetent son Brian were not that.
But the Dune series isn't Frank Herbert's best work. I'd put at least Destination: Void, Whipping Star, Dosadi Experiment, Hellstrom's Hive, and Eyes of Heisenberg above it, both for scope of ideas, character development, and pacing.
Dune most of the time meanders aimlessly through the desert, eventually coming up with a memorable scene, and Dune Meshuggeneh (#2) and Super-Babies of Dune (#3) are the least interesting books Herbert ever wrote. The others are all far more tightly written.
His short story collections, mostly about the ConSentiency setting (I want a chairdog!), are fantastic. And for sequels, the Bill Ransom co-authored Jesus Incident, Lazarus Effect, Ascension Factor are good stories of Humans under a deranged AI that thinks it's a god: Good lessons for the coming times.