Anima Ex Machina: Extra #1 [Time Setting]
AEM is considered to be slightly AU because it takes place in the present day (according to canon). The problem with that? Obviously, Hoenn isn't canonically overrun with alien parasites.
To be specific, AEM branches off of Diamond & Pearl -- as in, it's set in the anime universe at the time that Ash is going through Sinnoh. Outside of Hoenn, Ash experienced a few weeks of quarantine in Hearthome, imposed by the government on all traveling trainers to ensure that the "mysterious epidemic" didn't spread. When it was clear that the invasion was confined to mainland Hoenn, the quarantine on all other regions was lifted, and Ash was allowed to continue on his way. Ash, not being one who pays much attention to national news, didn't think much about it beyond that. At the start of the fic, he was focused on training for his sixth badge. All of the events of the Sinnoh arc otherwise occur as they did in canon. Team Galactic has absolutely no interest in the ixodida (although Cyrus cites it as another reason why the world needs to be destroyed and remade by Dialga and Palkia), and neither do the Sinnoh gym leaders or Ash's traveling companions. (Jessie, James, and Meowth are included in this statement. They also don't know that Giovanni gave them their assignment in part to keep them out of the way of the ixodida-related operations.)
The only main character who might have been affected, besides Tracey and Professor Oak, was May, but her family was evacuated to a refugee camp in Ever Grande just before the quarantine was imposed. There was a week in which all three of her family members as well as their pokémon were under careful inspection, but they're otherwise safe. May has considered rejoining her family, but she was encouraged by various parties to remain in Johto.
To go a bit deeper, five years have passed since Ash left Pallet Town. (Consider each region to be one year in length except Ash's journey through the Orange Islands and through the Battle Frontier, which were a year combined.) It's thus been five years since Ash met Bill, which gave the latter time to develop his reputation further. He and Lanette invented the Storage System in the interim. It's not in widespread use compared to Akihabara's system, although it's gaining popularity for its convenience. Additionally, Bill has perfected his techniques of using costumes in lieu of traditional research practices.
On a similar subject, dates. The Pokémon World is considered to be the same as Earth, only with advanced technology and pokémon. Thanks to humans' desire to tame the mysterious creatures that shared their world, people have developed methods of converting matter into a more compact form, and from there, humans sought to make every aspect of their lives easier. In other words, a lot of technology that exists today is because of the poké ball and the concepts of becoming a trainer.
Or in shorter words, the story is set in 2002. (Ash began his journey in 1997, so five years after that is... yeah.) There will most likely be what sounds like anachronisms in terms of technology, but the reader should keep in mind two things: first that technology developed differently in their world and second that at least two of the main characters are genius inventors.
Even more specifically, the story begins in October. It's only been a couple of weeks since the start, so it's right around the end of the month as of this writing (i.e., which coincides with chapter 11).