The mention of alternate universes is, actually, a rather genius way to explain the retcons of Pokemon in-universe. "There's a universe where Mega Evolution was never discovered" equally means "there's a universe where pre-Gen VI games are the canon." Which could be expanded to just about every retcon. Every generation could be considered its separate yet somewhat connected universe, and every version of the game its own reality. And for that matter all continuities to join together in one massive multiverse.
I honestly didn't think they'd try to explain these kind of issues without saying "its just a game, you can just relax." They actually made what amounts to a fan theory canon. I wonder if they'll do so for other aspects, like say certain unoffical Pokemon relations. This also may go to explain why Pokemon known to be one of a kind happen to appear in more than one reason-it is, but you live in a universe where it was there instead of here. So, how many universes are there based off the game alone?
*OG Timeline: The original games, Red/Blue/Green. Their version of Gold and Silver may exist, but Red would be fought with his main team member being a Venusaur, Charizard or Blastoise. Some post-Kanto Pokemon, if they exist here, could have different types and evolutions...for example the Dark type may not be here and Umbreon could be a Ghost who evolves through a Moon Stone or something. For the sake of things, we'll now say that each version is a different universe. So there are three similar universes with this timeline
* Yellow Timeline: First there's Pokemon Yellow, and then 3 years later Gold/Silver/Crystal. All three versions share the events of Pokemon Yellow in common, specifically diverging when Red has the team you see. Pokemon Stadium 2 could be a universe where Red got a different team or something. Whether or not it has Hoenn+ timelines is unclear. Its Groudon and Kyogre may be more docile because of the lack of an ability mechanic
* Ability Timelines: All universes with the Berry and Ability mechanic, but not the Mega Evolution. The Kalos War never happened here. Judging from Birth Island, Deoxys may have crashed much earlier and ended up there. Here are some guesses in what the timelines of this universes are like
** Pokemon FR/LG is concurrent with RSE. 3 years later a Sinnoh game could occur and could've happened, but you would face a Red with a different team. After several years we have B/W(they mention the villanous teams that failed), and 2 years later B2/W2. In B2/W2 of this timeline, Red would probably have a different team
** An unseen Pokemon Yellow, in order to fit with what you fight in HG/SS via Red.
** Assuming there is only one Weather Trio in the universe, then the full events of HG/SS universe does not have the events of the RSE timeline. Since the creation trio control time and space, they can be explained away as being captured in their relative future/past and escaping
* Mega Timeline: The current universe, of Gen VI. Mewtwo was found in Kalos' Unknown Dungeon, with primals existing
Going by this, these are the paths of the following timelines. Note that each independent version would be considered its own timeline
* OG Timelines-Red/Blue/Green(3 timelines)
* GBC Timelines-Yellow-3 years-Gold/Silver/Crystal(3 timelines)
* Ability Timelines A-FRLG/RSE-3 years-Altered HGSS/Canon DPPt-Many years-BW-2 years-B2W2(50 timelines)
* Ability Timelines B-Altered Yellow/RSE without the trio-3 years-HGSS/DPPt-Many years-BW-2 years-B2W2(10 timelines)
* Mega Timelines(as of now)-XY-Unknown time and order-ORAS(4 timelines)
So by my calculations there are 70 different game timelines. So what about the anime? Well for starters we know that the movies, with the exception of the first and 16th movie aren't canon because they aren't mentioned in the main storyline. However those two movies serve to form a contradiction-they have two different Mewtwos. It is impossible for them to co-exist, since Mewtwo's existence was kept completely secret. So what if they exist in two timelines? One where Mewtwo was created by Team Rocket, and another where it was made by parties unknown. Another factor is that Serena plays a major role in Ash's childhood, when nothing hinted at this. While retcon is the answer, Zinnia's explanation gives an in-universe answer. Both universes have Ash possessing identical teams, but for other characters things aren't confirmed fully until they re-appear with all their Pokemon
* The original timeline, which goes from the beginning to at least the end of Sinnoh. Mewtwo was created by Team Rocket, and Ash did not know Serena. From it diverges non-canon movies(2-9 and 13), and a three part trilogy of movies(10-12) serving as its own full timeline. So there are 11 timelines
* The Electric Tale timeline, and other mangas of the anime
* The current timeline, where Ash knows Serena and Mewtwo was created by another party. Diancie has a main series connection, so no divergence. M18 may be not referenced, or it may and in this universe it diverged when Rayquaza was born black