After reading the first four Dune books, and watching The masterful adaptation of the first half of the first book...

I thought what if Equestria would be what became of Earth after humanity had abandoned it for over 25,000 years?

And that after the Butlerian Jihad.

The Rise of Paul Atreides.

And the death of the God Emperor.

And during the scattering... Humans that where scaping the collapse of the God Emperor's empire, by dumb luck, after they completely forgot about it's existence over thousands of years history, find Earth again... And on Earth there are Ponies.

Humanity arrives at their world of origin, and at first maintained a tense situation where they decided to stay still and avoid the ponies for their safety.

Then humanity finally created a means to communicate with the Ponies... They then give them plenty of technology. But most importantly they warn them... They tell them their history, and warn them to not become like them... And they also tell them to always be weary of the tall ones they so cheerfully bow to...

----------

Basically its about humanity not being monsters, or saviors. But bitter teachers to ponies, warning them against the many mistakes that lead to the Butlerian Jihad, and eventually the 4,000 year Tyranny of the God Emperor.

It isn't an adventure, or an action story.

But a Science Fiction Tragedy where ponies learn from our doomed species...

In all the story at first would be a tense game of poker, with everybody and everypony scrambling to effectively make first contact without anyone blowing anyone else up. (Though humanity in this end would curb-stomp Equestria and the nations residing in the rest of the planet in mere hours. They just do not want to enter a war after 4,000 years of Atreides rule, and had simply had enough of everything that has happened.)

Then a cynical humanity tells the story of Paul Muad'Dib the Prophet, and the rule of Emperor Lato the Second. And inadvertently place the seed of doubt in the ponies minds.

After which Twilight reevaluates herself fearing what she may become if left unchecked. And thinks that even if she isn't a tyrant, how can she be sure that in the future there won't come a successor to the throne of Equestria that is one?

If I may ask the following questions:
1. When Mankind returns to Equis (Earth), is it possible for a long term sustainable thriving colony to flourish that can last generations?
2. If threatened by enemies in equis, are the human inhabitants prepared to wage war to defend themselves and demonstrate to the inhabitants of Equis why it's a bad idea to fuck around with them?
3. In correlation to the 1st question, will the humans in this long term, sustainable colony develop to not only to be a nation but a superpower player in equis almost equal to that of Equestria and the Griffon kingdoms?
4. How will the humans diplomatically relate to the nations of Equis?

7595981
1. Yes, Humanity even with the purging of AI have made up for it by the creation of Mentats, genetically altered human Supercomputers, which are simply humans that can think at the speeds that AI used to. And even though they have long banned the Spice Mélange they have allowed themselves to have restrained navigation systems that replaced the Guild Navigators (which heavily relied on Spice to device safe routes through space, while using space folding drives. They have the technology to quickly create a long term sustainable and thriving colony on the planet granted that they have enough land, which they are fully capable of making it artificially fertile if found to be unfertile.

2. It would be a massacre. While humanity had adopted the use of swords again do to the nature of energy shields that make projectiles useless, and would create small scale nuclear explosions when impacted by energy weapons. They have highly advance weapons on ships, and structures. Like Auto MAC Gun batteries, Lass Guns both in personal weapon size and large spacecraft sized, Missiles from large ones designed to destroy interstellar spacecraft to micro missiles designed to destroy small vehicles, not to mention Nukes and Bio Weapons. But that is the thing isn't it. They aren't going to attack first.

3. They will become one without even trying. Not through warfare but by simply showing up in large interstellar spacecrafts. Not even the Griffons are stupid enough to provoke a star-fairing species.

4. Humanity would for the most part simply try their best to bribe the nations of Equis to let them have several islands around the planet, and to also allow them to trade and travel freely among all those nations. The bribes will be technology, in exchange for human science, and the knowledge to replicate and produce human technology they ask that the nations of Equis do not attempt to enter into conflict with humanity, for their safety, and not theirs you see.

They will try not to overpopulate the planet, and instead they will try to build orbiting colony space stations across the solar system once heir population density reaches a certain point. If the Nations of Equis are willing they might allow free travel among them once they are constructed.
------------------------

If you notice all of this, it's not so out of much kindness but manipulation. They are purposefully forming a neo-cargo cult in which the more primitive Nations in Equis will simply be easy to manipulate and use to their leisure.

Questions pt. 2:
1. Will Mankind continue to innovate in the scientific and technological realm as well as industrial?
2. How will humans receive magic? Will they look down to the point that they hunt down those who wield it naturally (regardless of bad or good reasons)? or even better, see it as a new field to innovate with game changing implications?
3. How will Mankind's presence affect Twilight sparkle and her friend's lives?
4. How will harmony receive Mankind's return to Equis (Earth)?

7596473
1. To a certain degree. They no longer have AI, but they would innovate in everything else, and would use Mentats for the things that are expected of AI. They would innovate and continue till the point they can create worlds. But they would also continue to steer their own evolution, this time not only through selective breeding, and genetic enhancements, but also seek to become capable of things that can be considered Magick.

2. I may have to refer you to the Ultimate Guide to Dune series, but they would look at Magick with awe, and might also try to bribe ponies into getting them corpses they can study and experiment with to see if they can bring the old Myths of Sorcery to life. In all they would not be able to use Magick, right away. But within a generation of humanity returning children will be born that can use Magick. Humanity relies on prescience heavily, something only thought to be from the realm of Magick back in our time. And have synthesized the Spice Mélange, they have Spice. Imagine what a Unicorn can become if exposed to Spice?

3. This is after the show.

Twilight is the ruler of the wealthiest nation on Equis, and has a genius scientific mind, At first she would be exited, but as she learns more and more of humanities' history, and their history after they reached the stars... She starts to feel afraid for her subjects, she had seen "Our Town" and humanity had perfected Cults to the point of Leto's Rule. She fears that one day either her or a ruler on Equis will become a Tyrant that will be seen as a religious idol, and what terrible things somepony with her power can really do.

Applejack would be suspicious of their intentions, as she should be. But as she understands how much superstition and the shadowy machinations of groups like the Bene Gesserit, she would see why humanity had accidentally stumbled into Equis. What dishonesty and manipulation did to humanity would tell her one thing. That she could not allow humanities fate to be the fate of Equine and all other Sapient life on the planet.

Rainbow Dash had to be restrained from starting a First Contact disaster. She will later be approached by human scientists to scan and take genetic samples of her. Unbeknownst to her human scientists began to make Gola's of her to understand the nature of Pegasus, and particularly her Magick Propulsion. To see if it was possible to have aircraft that can defy the laws of physics as easily as she can.
----------
I ran out of ideas. I do not have the answers yet.