(Red/Blue)Yellow, (Gold/Silver)Crystal, (Ruby/Sapphire)Emerald, (Diamond/Pearl)Platinum, BlackWhite/BlackWhite2 are all from a different universe(A). A universe where Mega Evolution and Z-moves does not exist
LeafGreen/FireRed and HeartGold/SoulSilver is also from a different universe(B), however, still a universe where Mega Evolution and Z-moves does not exist.
X/Y, Omega Ruby/Alpha Sapphire, and Sun/Moon, are all from a different universe(C). A universe where Mega Evolution and Z-moves exist.
Additionally, Ultra Sun and Ultra Moon is also from a different universe(D). Different from the 3 that we've mentioned.
Although, we can say that in Universe e:
- Universe C/D Giovanni is present present.
- Universe D Lysandre is present.
- Universe B/C Cyrus is present.
- Universe A/D Maxie and Archie are present
- Universe C Lusamine would not appear of course, but Universe D Lusamine.
Why Universe C/D Giovanni?
- Red already once disbanded Team Rocket. Additionally, when Giovanni came back again, Gold/Ethan disbanded the "new" Team Rocket. The same can be said for universe B for HeartGold/SoulSilver. Plus, he now has a Mega Stone, unlike the first 2 Giovannis which doesn't even have knowledge about Mega Evolution.
Why Universe B/C Cyrus?
- The Cyrus from the universe A (original) disappeared in the Distortion World of Universe A. Unless shown to have Z-move or Mega Evolution or not, we can not have a certain answer.
Why Universe D Lysandre?
- The Lysandre from universe C (original) died from the explosion of the ultimate weapon. He can't be from Universe A or B either since he's shown to have a Mega Gyarados where Mega Evolutions does not exist in Universe A or B.
Why Universe A/D Maxie / Archie?
- Notice the appearance? It's from Ruby/Sapphire/Emerald. Why not " B or C"? Universe(B) is the remake universe but Mega Evolution still does not exist. Universe C has a different Maxie and Archie and Mega Evolution exists. Unless shown to have Z-move or Mega Evolution or not, we can not have a certain answer.
Why Universe D Lusamine?
- Ultra Sun and Ultra Moon happens on a different universe(D). Different from Sun and Moon's universe (universe C).
We still have no info about Ghetsis so we can assume that it's Universe A Ghetsis, unless proven or disproven.
Unless everyone is from another universe (E) which would make another question.
Legend:
Universe A - Original
Universe B - Remake Universe but without Z-move and Mega Evolution
Universe C - Alternate Universe(1) where Z-move and Mega Evolution exists
Universe D - Another Alternate Universe(2) where Z-move and Mega Evolution exists
We'll also have to take note that only the third games such as Yellow, Crystal, Emerald, and Platinum is the canon-est one of all the games for those that have 3 games.
However, we would like to also see this quote from Zinnia from Omega Ruby and Alpha Sapphire;
"My people know it. From generation to generation, we pass along the lore about the distortions in the world … And about the existence of another world, which we have long observed to be just like this one and yet not the same…
That’s right. A Hoenn region that’s almost exactly like this one we live in. Filled with Pokémon and people like us. A world where maybe the evolution of Pokémon took a slightly different path, where Mega Evolution is unknown… A world where that war 3,000 years ago…never happened. A world where the ultimate weapon was never even built. And in that Hoenn of that world… What would happen if one day, out of the blue, a meteoroid appeared? What would happen to the people of that world, without the technology to destroy the meteoroid or the power to warp it away?"