Omnius was the reason Paul couldn't see the Golden Path
He/It (Hit?) started humanity on the path to salvation and the first being invisible to prescience was actually Leto II and his goal was just to protect humanity from AI prescience.
Paul canonically didn't see Leto II - until his children were born, he only thought he was going to have a daughter. Of course, he hadn't seen Hasimir Fenring either - and for much the same reason!
The Butlerian Jihad never happened.
The Dune universe was well on its way to being another usual scifi universe where technological manufacturers ruled over everything. To gain more power, the Bene Gesserit convinced the populace that technology, especially the sort of AI that was hard for the Bene Gesserit to control, was a threat to all humanity. With their typical brainwashing powers, the Bene Gesserit carefully gained more and more power by forcing all of humanity into becoming Luddites. Later generations of Bene Gesserit carefully spread the story of a war against intelligent machines to keep the population at large from ever attempting to revive production of advanced technologies, producing an easily-manipulated society that's essentially the Dark Ages, but IN SPACE!.
Except for the fact that we've seen the Jihad from a first-person perspective.
Only if you count the non-Frank Herbert prequels as Canon.
Part of the storyline in the last two books is that the Bene Gesserit have never exercised that level of control over humanity, and that they have to do so to stop the Honored Matres. Not to mention that the history of the early Imperium seems to be fairly well remembered by most characters in-universe.
It doesn't just have to be the Bene Gesserit either. The empire and a lot of the Houses Major could have been in on it, because they would want an excuse to quickly band together and put down any rebellion against the feudal order, not unlike the Concert of Europe of the early nineteenth century. If the industrial workers of Giedi Prime decided to establish a dictatorship of the proletariat, the Emperor and the Landsraad could just scream "Robots!" and put it down (possibly even with atomics, if necessary). Any steersman, or proto-steersman, would have naturally also gone along with the plan.
Arrakis and the Sandworms were created by Omnius
Knowing it would be overthrown, Omnius made an alternate means to provide humans with interstellar travel and thus ensure species survival. He may have been a rapacious worlds-conqueror, but he wasn't an Omnicidal Maniac. A universe without humans to conquer wouldn't allow him to fulfill his prime function of conquering humans.
When its unprepared probe was eaten by one?
Dune is part of the Warhammer40000 universe.
Widespread religion, which is used to control the populace? Check. Tyrannical government? Check. Rage against thinking machines? Check. Psychic navigators on spaceships? Check.
Conceivably, depending on the year Dune is set in (which probably ranges from between 10,000 A.D. with the Butlerian Jihad, to 30,000 A.D. with Chapterhouse and Hunters of Dune), Warhammer 40,000 could be set after the Dune series, in a future where the spice melange has run out, and humanity is forced to use the series' chaotic and dangerous hyperspace to travel.
The year was 10,000 A.G. As in after the formation of the Guild to provide space travel again free of dependence on "thinking machines". That date doesn't count the unspecified span of time involving humanity's rise to wide spread space travel, technological collapse from the Butlerian Jihad, and planetary isolation before developing appropriate space travel to reknit the intergalactic empire.
It is also conceivable that the Dune continuity occurred prior to the revelation of the Emperor and the Great Crusade. The Butlerian Jihad would have been the suppression of the "Iron Men", the AI that had risen against their human masters. The events of Dune would have taken place in the Age of Strife, which would be longer than currently stated in the 40k timeline, but this can be explained as patchy and inaccurate records. Towards the end of the Dune timeline, the events that led to the rise of the Imperium would begin occurring, such as increased warp storms due to the birth of Slaanesh, and increased amounts of Psykers and mutants.
And Paul is the God-Emperor.
Glossu Rabban Harkonnen wasn't as stupid or evil as everyone thought
He shows up in one or two paragraphs. Everyone says he's a stupid brute, and then he gets his head cut off. We don't know much about him. Perhaps he wasn't as dumb or evil as everyone said; maybe he was some horribly disgruntled Harkonnen relative or something like that.
He was probably one of the first to notice the potential threat of the Fremen, a threat pooh-poohed by his 'far more cunning and intelligent' uncle Baron Harkonnen and ignored by Piter De Vries.
He spotted a threat Piter missed. Perhaps he's a latent Mentat?
Jar Jar Rabban, you're a genius mentat!
And he managed to live to be almost sixty while being a Harkonnen and having everyone gunning for him.
Judging by the book, I'd say he was just a simple man, and not being fully involved in the machinations all around him, focused on his own life and tasks. He was Regent of Arrakis before the events of Dune, and heard the reports of the officials and the Sardaukar during the coup. He wouldn't be so quick to dismiss the Fremen as a threat because he'd have little else to focus on.
Following on that, Glossu Rabban Harkonnen survived the events of Dune
He was smart enough to get an off-screen "death", rather than his cousin's in your face and on-page vicious stabbing.
Time exists as seven Ages. In each Age a specific set of events always occur, even if other details vary. There are certain people, souls, who always appear to drive these events. One of these is basically the Messiah who comes about whenever humanity is in dire need, and usually heralds the end of an Age- this soul is known as the Dragon.
The First Age, our age, is implied to have ended in brutal warfare (the Machine War). John Connor was the Dragon for the First Age, and saved the human race while ushering in the Second Age.
We know from Terminator Salvation that there are humans who don’t believe the Resistance can defeat Skynet. A group of these people conspire to go back in time in order to escape the machines. They succeed, but mess up the space-time coordinates and end up on the planet that eventually becomes Coruscant.
During the Yuuzhan Vong War, a group of humans flees the galaxy. They end up in another galaxy utterly devoid of sentient life. They eventually build sentient machines. These machines enslave humanity (another repetition of the BSG Cycle). The humans rise up and annihilate the machines in a two-generation galactic war called the Butlerian Jihad. This causes the humans to forsake all powerful computers- including ones that could calculate FTL jumps. This leads to the Dune universe relying on spice that allows them to go faster-than-light.
Back to The Start:
There are two ways to end up back at BSG, one from Star Wars and one from Dune
Star Wars Path:
Sometime in the millennia after the Yuuzhan Vong War, some great cataclysm utterly devastates the galaxy beyond all repair. Survivors flee to another galaxy and settle on a large habitable world. They call this world Kobol and the Thirteen Lords of it are the last members of the Jedi Order or other Force-using faction.
During the Butlerian Jihad, some humans flee the galaxy and end up on a planet called Kobol. It’s Thirteen Lords are the last Spacing Guild Navigators.
Bene Gesserit Prana Bindu muscle training is actually Hokuto Shinken or some variant thereof.
Many students and members of the Bene Gesserit perform feats that can only be described as superhuman, through a combination of spice ingestion, muscular training, and selective breeding. They are also quite familiar with the ways of the Fremen, a desert people, and even managed to create several myths to benefit members of their sect and further their plans. Consider the following scenario: Kenshiro, the 64th FOTNS, is tasked with protecting and rebuilding humanity, however he knows he cannot do it himself, and he knows that the old way will not work. He also knows that there are techniques and disciplines in the Hokuto and Nanto styles that, if taught to multiple people, might create a powerbase that will help the world recover and take a new path, among them being healing (both others and self), skill reading, and body metabolism management (how he traverses the desert with ease). So he starts a group, and doesn't quite teach them everything, but enough to keep them from becoming savages and assist in the reconstruction of the world. The sign of this group is a hawk, one of Kenshiro's constant companions. He decides to train the women primarily in the arts of body regulation, healing, and body reading, but continues the tradition of the Fist with men only. As time goes on, the hawk becomes the crest of one of the group member's family (the Atreides), and they either abandon the tradition of the fist, it is decided that the technique must be abandoned, or it is sealed from them in such a way that after two or three generations, they forget that they are descendants of Kenshiro's social reconstruction project. The Bene Gesserit however, continue their training, and update it first with bastardized versions of Hokuto and Nanto that have appeared in other FOTNS media, and later on methods and techniques from other cultures. However, none of them can quite achieve the power levels of a Quizat Haderach, in part because the really destructive parts of Hokuto (the universal Ki manipulation, predicting an opponents movements, etc etc) were only taught to the men, while the BG are either taught Nanto or a Hokuto offshoot. Once one becomes a Quizat Haderach, the entirety of the art becomes available to them, along with the improvements that the BG have made on their end.
And the Honored Maitres training is descended from Sexy Jutsu.
The Gom Jabbar...
...was testing the subject's obedience and controllability.
...was applied because Gaius Helen Mohiam just likes hurting people.
...wasn't actually poisoned. It's meant to separate humans and breeding stock. What's the good if you kill the breeding stock?
...Or it uses a selective poison that only kills those who have already had children.
To the Bene Gesseret, all people are breeding stock. She just said it that way to let Paul down easy, in case he failed he would think he was dying for a good cause. In reality, the Gom Jabbar test is for culling breeding stock.
If she had killed Paul, Gurney/Thufir/Idaho would have followed her back to Chapterhouse if necessary to make sure she was executed. It wouldn't make sense to actually poison the needle and risk accidentally killing him (even a Reverend Mother might be vulnerable to accidents, e.g. earthquake).
It's established in later books that it's actually pretty goddamned hard to kill a Reverend Mother by "normal" means. Not to mention the whole protection of the Emperor thing. And finally, they had a pretty good idea that Paul was a candidate for the Kwisatz Haderach, or in other words, a male truthsayer. Trying to bullshit him about a poisoned needle would have risked him getting smart to it and compromising the test.
If Mohiam had actually been stupid enough to murder the Atreides heir in his own home... the question would simply be which of her Imperial protection being revoked or Chapterhouse handing her back to Leto happened first. Not to mention the complete PR disaster it would be for the Bene Gesserit in general.
Erasmus killing Serena's baby started the Butlerian Jihad, which created the necessary conditions for all the events afterwards. UPDATE: Also, any possible manipulation by Omnius was either Erasmus' doing to start with or out of a realization of what Erasmus had set in motion.
...So where's the WMG? You're merely describing the events of the books.
Leto II didn't count on Duncan Idaho being the ultimate Kwisatz Haderach.
Or maybe Leto II was helping him become that. It's been a long time since I've read God-Emperor of Dune, but there's no way Duncan Idaho could have gotten where he was without Leto II constantly re-hiring him and supporting the Bene Tleilaxu's efforts.
Tons of colonies of humans originally from Earth? check.
This is why nukes aren't used in Dune even though it's mentioned they have them! With each cycle humanity goes longer before nuking itself back to the dark ages. By the time Dune occurs that cycles probably happened on tons of planets. The others aren't going to grow the balls to try again for a couple millenia!
However, A Stone Burner is used in a later Dune novel and that definitely was a nuclear weapon. Not to mention the atomics Paul used to destroy the shield wall in the first book. And Salusa Secundus was rendered radioactive by a rogue house 8,000 years ago. They don't use nukes very often because the laws of Kanly forbid them, and offending houses are annihilated by the Emperor and Spacing Guild.
This is why the people in Dune know so much about Earth! Remember the Order brought the Memorabilia, which was all the knowledge they had up until that point, with them into space
Dune comes after Firefly
No aliens, nobles rule and the tech level fits for about 2,000 years before the Jihad.
The Golden Path began long before Leto II.
Arrakis is Earth!
According to Leto II, the sandworms didn't originate there, and sandtrout are thought to be responsible for destroying all the surface water. Humanity's ventures into space would have been very slow and dangerous before Melange was discovered, so it makes sense they were "close to home" until then. Also, any astronomical discrepancies (number of moons, gravity, mass, orbit) could be justified by tens of thousands of years of technological, ecological, and political events. Hey, so what if Frank said it orbited Canopus, what does HE know (anyway, enough navigators coulda moved it?).
So basically, it can be as long as you ignore every scrap of evidence saying it isn't?
Sandworms are nuclear powered
Arrakis orbits Canopus; a star only a few tens of millions of years old, at the most; this means that the concentration of U-235 in natural uranium must be much higher, because it hasn't had time to decay. The sandworms have no apparent source of energy other than the sand plankton, and, since the plankton only eat spice, they don't represent an energy input into the system. This means the sandworms have to be internally fueled by nuclear reactions; a sandworm collects uranium and stores it internally in such a way that it can control the reaction (possibly by regulating the distance between the masses). The heat from this reaction (somehow) fuels the endothermic internal processes they need to create chemically usable calories and output oxygen. This also explains why water sends their internal biology into overdrive; it functions as a neutron moderator, massively speeding up the nuclear reaction. Essentially, the worm has a very strongly negative void coefficient, and therefore has a power spike as a result of an "Acquisition of Coolant Accident".
The Kwisatz project was the second Bene Gesserit see-into-the-place-we-dare-not project
One: Several indications are made that the place Bene Gesserit Other Memory that terrifies them is male-line Other Memory.
Two: Two females are known to have had at least some degree of access to male-line Other Memory: Ghanima and Alia Atreides.
Three: Ghanima and Alia are both Abomination by Bene Gesserit standards.
Four: The Bene Gesserit place high priority on the termination of Abominations.
Theory-in-Conclusion: the Bene Gesserit at some point deliberately created what would later be referred to as 'Abomination' in an attempt to sidestep certain limitations of Bene Gesserit abilities (such as the inability to access male-line memory). While the project was to some degree successful, it went disastrously wrong in other respects (ref. Alia Atreides; compare Paul Muad'Dib) resulting in the 11th millenium AG Bene Gesserit reaction to Abominations.