Wait, wouldn't rain kill the sandworms and stop the spice flow, ruining the galaxy?
This point was driven home in God Emperor, wasn't it? The lush green vegetation and the accompanying rains were slowly killing off the Makers. The worms were much smaller and living in much more confined smaller areas of desert on the green Arrakis.
I got the first novel in hardback as a gift from my uncle when I was in 7th or 8th grade. I read up to God Emperor but never finished that book. I was reading God Emperor for a book report in Lit class. I got to the point where I stopped reading the book and left the book report off as a cliffhanger. I ended the report with "if you want to know how the story ends, you'll have to read the book. I got a really good grade on the report!
Years later I went back and read the entire series (as it existed at that time) up to Chapterhouse: Dune. I agree with your assessment that Messiah felt like a half-finished book, especially after such an epoch as Dune.