Now the long part... (takes a deep breath):
I wanted in fact to make timelines for most of the things in the Japanese side of this Omniverse, I am still on it, but here what I have got about connections between multiverses.
There is a Japanese Video Game series called Super Robot Wars that features crossovers between different mecha animes.
In a given Super Robot Wars game usually the world presented is a mix between the different mecha series, and the game is an adaptation of all the series at the same time. Obviously, the presented variation of the anime is not the canon one. And usually, the next Super Robot Wars game is a totally different universe from the previous one (but there are some sequels and "series" of like 4 games that continue one after the other). Usually a series is adapted in different games but the adaptations are different between them and mixed with other series diferently.
The thing is that this is a confirmed multiverse, since there is a character called Gilliam Jaeger that is said to be the same version in all of his appearances, travelling the multiverse. Aparently he originates from an older series by the same developer called Compati Hero series that is basically a SRW game but instead of Mecha series it has Gundam, Kamen Rider and Ultraman series (obviously the Gundam series overlaps with Super Robot Wars) but again, their versions are not the canon ones, since their plots are happening at the same time with the villains scheming together when in canon Kamen Rider and Ultraman take place in the present and Gundam enough into the future for the characters to call World War II "the Middle Ages".
Also, and very important, there was a Japan exclusive game called "Namco x Capcom" that was made by Banpresto, the ones that make SRW, and was basically SRW but with Capcom and Namco, so there is Resident Evil, Mega Man, Klonoa, Tekken, etc characters in a world were apparently all of their adventures happened or are happening now. Since not all series fit in the same universe they are like 5 different universes involved. I think that the Super Robot Wars characters that crossed over in the game were implied to be their canon selfs. TV Tropes I think that insinuated that the Xenosaga characters were the canon selfs pulled from the ending of their game (I don't know if their game ends with them travelling the multiverse, since it is like Evangelion but in video game, everybody says that is so great but nobody apparently understood the plot, so I was curious about playing it myself and don't want to spoil it for myself), so I am not sure about it, since TV Tropes is not the most accurate source. Then a SRW for DS featured the original, non-licensed, characters from Namco x Capcom and the Xenosaga characters (the same version from NxC, still, no idea if the canon one) arriving from their universes, reinforcing that the SRW and Namco x Capcom Multiverses are the same. Then, in 3DS, Project X Zone was released (even outside Japan) and it is something of a "Namco x Capcom x Sega", it continues Namco x Capcom plot, the licensed characters reference their meeting from the previous game and the Namco x Capcom and SRW Endless Frontier (the above mentioned SRW DS games) original characters are included as Namco characters. The sequel, Project X Zone 2, ads two (I don't know why just two, since the other companies have like 10 franchises each) Nintendo franchises to the mix: Xenoblade Chronicles and Fire Emblem. Xenoblade Chronicles is an spiritual successor to Xenosaga and to Xenosaga spiritual predecesor, Xenogears, all three are hinted to share a universe/multiverse. Fire Emblem HAS a multiverse, as seen in Fire Emblem Awakening DLC chapters and more titles. In Fire Emblem Fates there is a function were you can scan Fire Emblem characters amiibos and they appear in game in a conversation and leave a few goods. If you scan the Super Smash Bros. Robin amiibo a version of the characters appears, but the Fire Emblem Awakening characters (that traveled to this universe from their own) notice that this is not their Robin, and Robin mentions other fighters, hinting that he is the Robin from the Super Smash Bros. universe.
Cross Edge is another crossover game that features video game crossovers. I don't know if they are the canon versions or local versions of the characters. But crosses over Atelier, Darkstalkers, Disgaea, Ar tonelico and Spectral Souls. I don't have any idea about the last two but Darkstalkers adds this to the Omniverse because of Capcom. Atelier crossed over with other Koei Tecmo properties pulled from their universes in Warriors All-Stars, so some kind of Koei Multiverse made up of Ninja Gaiden, Dead or Alive, Nioh, Fatal Frame, etc is also here.
I remember that I forgot a few things but I am a little bit tired of writting so I will leave this here
I wanted in fact to make timelines for most of the things in the Japanese side of this Omniverse, I am still on it, but here what I have got about connections between multiverses.
There is a Japanese Video Game series called Super Robot Wars that features crossovers between different mecha animes.
In a given Super Robot Wars game usually the world presented is a mix between the different mecha series, and the game is an adaptation of all the series at the same time. Obviously, the presented variation of the anime is not the canon one. And usually, the next Super Robot Wars game is a totally different universe from the previous one (but there are some sequels and "series" of like 4 games that continue one after the other). Usually a series is adapted in different games but the adaptations are different between them and mixed with other series diferently.
The thing is that this is a confirmed multiverse, since there is a character called Gilliam Jaeger that is said to be the same version in all of his appearances, travelling the multiverse. Aparently he originates from an older series by the same developer called Compati Hero series that is basically a SRW game but instead of Mecha series it has Gundam, Kamen Rider and Ultraman series (obviously the Gundam series overlaps with Super Robot Wars) but again, their versions are not the canon ones, since their plots are happening at the same time with the villains scheming together when in canon Kamen Rider and Ultraman take place in the present and Gundam enough into the future for the characters to call World War II "the Middle Ages".
Also, and very important, there was a Japan exclusive game called "Namco x Capcom" that was made by Banpresto, the ones that make SRW, and was basically SRW but with Capcom and Namco, so there is Resident Evil, Mega Man, Klonoa, Tekken, etc characters in a world were apparently all of their adventures happened or are happening now. Since not all series fit in the same universe they are like 5 different universes involved. I think that the Super Robot Wars characters that crossed over in the game were implied to be their canon selfs. TV Tropes I think that insinuated that the Xenosaga characters were the canon selfs pulled from the ending of their game (I don't know if their game ends with them travelling the multiverse, since it is like Evangelion but in video game, everybody says that is so great but nobody apparently understood the plot, so I was curious about playing it myself and don't want to spoil it for myself), so I am not sure about it, since TV Tropes is not the most accurate source. Then a SRW for DS featured the original, non-licensed, characters from Namco x Capcom and the Xenosaga characters (the same version from NxC, still, no idea if the canon one) arriving from their universes, reinforcing that the SRW and Namco x Capcom Multiverses are the same. Then, in 3DS, Project X Zone was released (even outside Japan) and it is something of a "Namco x Capcom x Sega", it continues Namco x Capcom plot, the licensed characters reference their meeting from the previous game and the Namco x Capcom and SRW Endless Frontier (the above mentioned SRW DS games) original characters are included as Namco characters. The sequel, Project X Zone 2, ads two (I don't know why just two, since the other companies have like 10 franchises each) Nintendo franchises to the mix: Xenoblade Chronicles and Fire Emblem. Xenoblade Chronicles is an spiritual successor to Xenosaga and to Xenosaga spiritual predecesor, Xenogears, all three are hinted to share a universe/multiverse. Fire Emblem HAS a multiverse, as seen in Fire Emblem Awakening DLC chapters and more titles. In Fire Emblem Fates there is a function were you can scan Fire Emblem characters amiibos and they appear in game in a conversation and leave a few goods. If you scan the Super Smash Bros. Robin amiibo a version of the characters appears, but the Fire Emblem Awakening characters (that traveled to this universe from their own) notice that this is not their Robin, and Robin mentions other fighters, hinting that he is the Robin from the Super Smash Bros. universe.
Cross Edge is another crossover game that features video game crossovers. I don't know if they are the canon versions or local versions of the characters. But crosses over Atelier, Darkstalkers, Disgaea, Ar tonelico and Spectral Souls. I don't have any idea about the last two but Darkstalkers adds this to the Omniverse because of Capcom. Atelier crossed over with other Koei Tecmo properties pulled from their universes in Warriors All-Stars, so some kind of Koei Multiverse made up of Ninja Gaiden, Dead or Alive, Nioh, Fatal Frame, etc is also here.
I remember that I forgot a few things but I am a little bit tired of writting so I will leave this here
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