Oddly enough, I quite like God Emperor. I thought there were some interesting explorations (although it did its fair share of literary naval gazing too). I think what appealed to me was the evolution of the ‘establishment’. Dune initiated the overthrow of the old order, only to replace it with something arguably worse. It reminded me of tsarist Russia being overthrown by Communism - which ultimately led to little more than red tsars running the show. For all that things had changed, things tended to stay the same.
I suspect I may be in the minority here
Okay bear with me....but
God Emperor was really about Leto's plan to save humanity - but doing it by establishing a dictatorship that lasted about 4000 years with him at the top.
Let's start with Paul Atreides. Part of the reason Herbert wrote
Dune, I think, was to contradict the traditional heoes journey - be careful of wishing for a heroic leader. you may not like what you get! He's clearly the protagonist of the book and indeed, you the reader, have empathy for Paul against the Baron and the other scheming factions. Yet at the end, when the 'good guy' wins, it unleashes a jihad throughout the known universe. Millions and millions, perhaps billions of people are killed by fanatic fremen who blindly follow Muhaidib.
This is a good outcome?
What is somewhat worse is that Paul
knows exactly that this will happen, because he becomes Kwisatz Haderach and his powers of prescience. He can see the various futures; he
chooses this future.
After
Dune Herbert, I believe, wanted to move on and explore prescience further. What are the problems with seeing the future? So he gives Paul, and therefore his children, including Leto, the knowledge of the 'great threat' that will extinguish all humanity. What is this?
There's a hint from my reading from the system of Ix. I forget exactly when, but the scientists of Ix develop at some point an interstellar ship that does not require a navigator to safely travel between the stars. This, on my first reading, was a nice move, it changed the monopoly on travel that the space guild had, it complicated the politics. But I think it was more. Remember the navigators used a limited form of prescience to predict where obstructions were on their journeys. So in a sense Ix has developed a machine with limited prescience to replace the human element.
There's a moment in
God Emperor where Leto tells someone of his 'visions' of a possible future still open where humanity is hunted and destroyed by a prescient foe, the final humans huddled deep underground in bunkers listening to the ever increasing volume of machines burrowing inevitably towards them.
I think also we are supposed to think that the power that makes the Honoured Matres flee back from the Scattering into the old worlds is also this 'great threat'. Unfortunately Frank Herbert died before he could finish the book that was likely to describe the threat appearing. However from the book Brian Herbert and Kevin Anderson wrote, which I'm sure they used what Frank Herbert had prepared in notes and discussions, I think it was a great armada of thinking prescient machines - the technology banned and destroyed in the Butlerian Jihad but recreated (or survived and grown?).
Paul sees this future too. What does Herbert make him do? Well, further stripping away his heroic qualities Paul abdicates his responsibility to fight this threat. He forces the task onto his son Leto and essentially retires and dies (I think!). Paul really fails on quite a number of fronts!
So what is Leto's plan? His first important goal is to breed humans that his prescience can't see, humans that any prescience can see, so that they are immune to the great threat. The future where humanity is made extinct will be stopped. But he also needs to spread these genes around all humanity. How does he do this? He sets up a dictatorship. He stops all opposition, oppressing and keeping humans 'local', restricting technology, and all of this is held in place by an army of fish speakers. A female army he used to control and police everyone, it is fanatical and unquestioning - he can also use them as part of his breeding program.
He does this for ~4000 years. I think he needs to do this because he needs that amount of time to finally breed the correct gene-line, but I think it also builds up a desire for freedom in humanity. He knows that when he finally dies, his empire will be 'straining at the leash' to escape his stagnant dictatorship, will completely disintegrate and the Scattering will take place where vast numbers of people flee the old empire into uncharted areas, spread out and grow. With that he plants the seeds of the new humanity he has been breeding.
So in a way, Leto is a bit of a anti-Paul. He is actually aiming to prevent something terrible happen, it's just that he has to impose a lesser evil on human society to stave off something much worse ~10,000 years down the line. Worse, Leto is forced by his own father into this duty! I don't think Leto is intrinsically a bad person, so he must endure thousands of years of inflicting pain and suffering on humanity for a future that he knows he will die thousands of years before as well!