I’ve had a few ideas for AU settings. Most tend to be fairly different from the main timeline; One of the more severe examples being one I call the Echoes ‘verse where both Celestia and Luna end up going a bit mad and turning into Daybreaker and Nightmare Moon before battling to the death for the throne, and their battle is so intense that it splits the timeline into two, one where Daybreaker wins, and one where Nightmare wins. In the ‘Day’ timeline, we end up with eternal day, and over the course of a thousand years not only does the world get hotter and hotter until nothing can survive naturally, but magic itself has been drained away. To compensate, the ponies have developed very advance technology to create giant metal blocks that they live in like compact cities. In the ‘Night’ timeline, we have the opposite, eternal night with a world frozen over but ponies thriving with super-powered magic but tensions between the races so severe that they have to be separated into their own nations. Both timelines are ‘echoes’ of the main timeline, with the same ponies existing and holding the same names and equivalent jobs. Ponies of both timelines are affected by what they call ‘Fate’, which is a force that gives ponies their names and directs their eventual paths in life.
For a more traditional timeline, it is one that I call ‘One-Winged Angel’, where Cloudsdale is about twelve feet to the left. As a result, around the time when the first Sonic Rainboom happens, Fluttershy falls to earth due to Rainbow’s race, but is not caught by butterflies; The injuries are severe enough to seriously damage her spine, preventing her from being able to use her hind hooves, as well as taking out a wing and leaving her blind in one eye. Her family ends up having to move to Ponyville simply because Fluttershy is to terrified of living in Cloudsdale anymore in fear of falling again. During a game of kickball at school, where she just quietly stayed on the sidelines, a colt kicks the ball into the air where it hits a bird. Concerned, Fluttershy takes the injured bird home and nurses it back to health, and upon seeing it fly again, she decides she wants to help others so they don’t end up like herself, and thus decides to become a nurse. Due to having to deal with ponies as part of the job, she’s noticeably less shy than that point in canon by the time of the Summer Sun Celebration, though she still tends to keep to herself, though she does regularly keep in touch with Derpy Hooves, pretty much her only friend as Derpy was the one to find her when she fell and who visited her hospital bedside often with a fresh muffin each time.
When Nightmare Moon returns, Derpy takes her place to go with Twilight Sparkle, thus resulting in Derpy becoming the Element of Kindness. Another Element Swap is that Bon Bon ends up as the Element of Loyalty instead of Rainbow Dash, who never left Cloudsdale. Rainbow pretty much blamed herself for Fluttershy’s condition, and despite Fluttershy’s urging, never forgave herself. Instead of dreaming to become a wonderbolt, taking a job as a weatherpony in Ponyville to stick with her friend while she practices her tricks, Dash becomes rather aimless and ends up working in the weather factory, over time growing a fondness for the mechanics of the job as the many technical aspects take up all of her focus and allow her to forget about her own guilt.
The third AU that I’ve put serious thought into is one called Millennium, though that one is much larger in scope and only sort of an AU because instead of changing events or details in the canon timeline, it instead jumps one thousand years into the future, where Equestria is the neutral party between a long-running cold war between the Changeling Union to the sound and the militant Crystal Empire to the north, led by Supreme General Flurry Heart (long story). At this time, Queen Twilight has a new student, a stallion named Eclipse who was cursed with dark magic when he was a foal, who is sent to the town of Everfree to learn friendship (of course). Other characters of note would be Jade Edge, a Crystal Pony veteran of the very recent Griffon Civil War, Wrench Works and Spanner Works, two intelligent hippogriffs that run a toy shop, Ventriculus, an easy-going changeling who works at the local bakery and (unbeknownst to the others) is also a veteran on the opposite side of that civil war, Kular’t, a blind griffon history enthusiast that works at the museum inside the Castle of the Two Sisters, and Rose Quill, a unicorn that writes romance novels.
I’ve had plenty of ideas like these for a while, I just need to do something with them at some point.