I absolutely agree. Children of Dune and Dune Messiah are by far the worst. The series picks up with God Emperor of Dune, and my favorites are the last two: Heretics of Dune and Chapterhouse Dune.
The original Dune book was also good, but overrated compared to the last two in the series.
I'm the opposite, I found the books in a steady decline from book 2 onward. I thought the last two were terrible. And the new books by Brian Herbert were largely unreadable. But we all have different tastes.
5th and 6th are also interesting in that they explore the Sects and universe more in depth.
Personally I found 2nd and 3rd books the worst.