Well, I suppose the best place to start would be Johto, not only because Johto is very fond of its festivals but also … because I’m from there, so naturally, I would know a thing or few about Johtonian holidays.
But yes, Johto is big on holidays throughout the year, and autumn is the temporal home for quite a few. For starters, there’s of course the Autumnal Equinox Festival, which is when we honor our ancestors and give thanks to nature for the upcoming harvest. There are also minor holidays for the harvest throughout the region, depending on which town you’re visiting. The coastal towns tend to bookend the season with two separate holidays (Autumnal Equinox and the Fisherman’s Day holidays) to ask/thank Lugia for safe waters to fish and sail in before the weather gets too rough and bitter for doing either. In the more mountainous or farming-oriented communities, you tend to have more festivals, often geared towards asking/thanking Celebi or the legendary beasts for blessings. (A side note: You only honor Ho-oh; you never ask Ho-oh for blessings. And you do this during the summer solstice, not the autumn. Autumn is considered to be the beginning of Lugia’s domain more than Ho-oh, but that’s an entire side point.)
And of course, you have Goldenrod, which considers itself in a historical sense to be both a fishing and a farming community, which means it celebrates all of these (or at least it uses this as an excuse to celebrate all of these, as the Goldenrod custom is to use any excuse possible to throw a party).
Either way, these are celebrated with feasts centered around the bounty in question (fried and raw fish for the fishing communities; fruits, vegetables, and grains for the farming), and offerings are often made to local shrines for the deceased.
Then, after the harvest festivals, you have the Respect for the Aged Day, which I admit is more of a media-based holiday (in that you will often see the news or hear the radio interview the elderly during this time), but it’s also often celebrated (at least in Johto) simply by visiting the elderly members of your family. There is also a holiday meant for children (Shichi-Go-San), which is often considered a rite of passage: it’s when Johtonian children pass from young childhood into middle childhood, which might not seem like much to an outsider but essentially means you begin your preparations for a pokémon journey (or adulthood) at this age. So you’re dressed in traditional clothing (for the first time, if you’re male or a younger female) and taken to your nearest shrine to pray for luck and prosperity. As a note, Shichi-Go-San is not to be confused with Kids Day, which is a general celebration meant to honor and respect children, rather than a rite of passage from one stage of life to the next. Kids Day is celebrated in May, so it’s more of a spring/summer festival than an autumn one.
Finally, there’s also Thanksgiving, which is technically a labor holiday outside of Johto. Inside of Johto (particularly Goldenrod), it’s often celebrated much like it is in Unova, as another harvest holiday, because Johtonians are not at all ashamed to admit that they’re fascinated by Unovan culture.
This is, of course, just speaking in terms of broadly celebrated holidays. Some towns in Johto have additional holidays that they celebrate locally, such as one town dedicating an entire festival in November to wobbuffet. No particular reason; it’s just that this specific town really likes wobbuffet.
Other Japanese regions—including Kanto, Sinnoh, and Hoenn—share many of these holidays because, quite obviously, we’re all one country (which means that state holidays apply to all of us, and we all share a baseline culture), but attitudes towards them tend to vary by regional culture. In Sinnoh, there’s a particular emphasis on local harvest holidays and the autumnal equinox because it’s largely a farming region, and even then, many of its stories center around giving thanks to pokémon. This is not only a reference to Shaymin but also to the Sinnoh folk story about returning the bones of the animals and pokémon you’ve eaten to the wild to be resurrected. It’s important, in other words, to give thanks and respect even the pokémon you intend on consuming in order to ensure the balance of life is maintained—or at least, this is true for a Sinnohan. That having been said, Sinnoh does indeed have one other holiday not shared with the other regions, and that is Gratitude Day, to honor Shaymin and the Sinnohan ancestors.
Then you have Unova, Kalos, and Orre, which as western regions, tend to celebrate similar holidays due to the shared heritage of either their founders or their countries themselves. For example, all three celebrate their military veterans in a holiday that’s called Veterans Day in Unova and Orre and Armistice Day in Kalos. Both holidays are celebrated on the same day (November 11) and in similar fashions because ultimately, they share an origin (World War I specifically, but World War II and the Great War all play important parts in those regions’ histories).
On a lighter note, though, each of these regions also celebrate Halloween, although there’s far more emphasis placed on the fun of it (that is, costumes, candy, and horror) in Unova than in elsewhere. In Kalos, it’s often celebrated just after a festival dedicated to gourgeist, the Gourgeist Festival. In fact, the Gourgeist Festival is often when most of the customs associated with the Unovan Halloween are observed, particularly the costumes. Conversely, in Unova, Halloween is celebrated just before the a number of holidays meant to honor the dead, including the Wishing Bell Festival (if you live in Mistralton City) and Day of the Dead (if you’re Mexican-American). As a side note, Day of the Dead is a very fascinating holiday with its own history, and its customs tend to vary from community to community. For example, in Castelia, there’s often a parade, whereas in relatively quieter towns such as Nuvema, celebrants simply bring offerings for the dead to their local cemeteries. Sometimes, these celebrations also incorporate Halloween and other autumn festival customs as a means of “rolling it up into one,” so to speak.
Finally, there’s the second biggest autumn holiday to Unovans and Orreans, Thanksgiving. Supposedly, this is meant to be a holiday dedicated to the story of Unova’s founding, but really, it’s more of a modern-day harvest festival, in which the Unovan family gathers together over a massive feast (often involving turkey, pumpkin pie, and awkward political conversations). Or at least, that’s what it is from my understanding. This is not to be confused with the Grand Harvest Festival, which is a Unovan festival in mid-September meant to honor a time when Unovans learned to settle their differences and work together in peace to restore and protect the nature around them. On the other hand, this holiday is followed quickly by the ones where Unovans fight over resources to the detriment of their fellow Unovan, so I suppose one could say these holidays are unintentionally related.
Alola technically is part of the same country as Unova and Orre and thus shares many of its holidays, but because Alola possesses a very unique culture with a separate history, less emphasis is placed on the state holidays and more on the local ones. In Alola, this means that there’s a lot more emphasis placed on honoring the tapu. While each of the tapu have their own holidays, Tapu Bulu is especially celebrated throughout the autumn season. Each of the islands has their own separate festival for them, but on Ula’ula Island, Tapu Bulu’s home territory, the Tapu Festival is a week-long celebration in mid-November. Some of the customs include leaving offerings within the ruined buildings of Tapu Village (or Ruins of Abundance, if you’re willing to traverse the often unrelenting Haina Desert), as well as the standard battles (often at the top of Mount Lanakila) to entertain the tapu. The latter also involves a series of challenges staged through the Lanakila cave system that participants must get through to reach the top of Lanakila.
And finally, there are a few globally celebrated holidays, including Diwali (the Hindu festival of lights) and the Jewish High Holidays (primarily the Jewish new year Rosh Hashanah and the Day of Atonement, Yom Kippur). This isn’t to say that the above-mentioned holidays—Day of the Dead, for example—aren’t celebrated outside of the regions mentioned above. It’s more to say that practically every region has a significant population of Hindu and/or Jewish people that these holidays are recognized on some level by practically every region.
Of course, this just scratches the surface because the world is such a vast place with so many different peoples and customs that it’s impossible for me to cover them all. However, if you’d like to mention your own region’s autumnal holidays, by all means, send an ask!