When people say “Dune Messiah” isn’t as good as “Dune” they’re really missing the point. It isn’t a sequel to “Dune”, it’s just the rest of the book. You see, “Dune” is divided into three sections (Dune, Muad’Dib, and Prophet) but it should have had a fourth part called Messiah.
"Dune" has a seemingly happy ending, with Paul Muad’Dib Atreides avenging his father and ascending to the emperor’s throne. But throughout the book Paul (who has the gift of prescience) worries about a "terrible purpose" the universe has in mind for him. He sees a jihad sweeping through the universe, killing billions in his name.
"Dune Messiah" picks up twelve years later and shows what happens after the jihad is over. Paul is emperor, but he can’t control the religious zealots who have turned him into a god. His efforts to transform Arrakis have angered Fremen who long for the old days. A conspiracy formed by the Bene Gesserit, the Tleilaxu, and the Spacing Guild hopes to depose him.
Some look at “Dune Messiah” as a depressing follow up to the original, but if you read “Dune” closely it’s clear Frank Herbert never intended for Paul’s story to have a happy ending. That’s why, even though it was released as a separate novel five years later, it’s much better to look at it as the conclusion to “Dune”.