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1 and 3 take place at the same time.
2 and 4 take place at the same time.
6 includes gen 3 remakes, so it would make sense that it takes place at the same time as 1 and 3 but...
5 takes place after 1/3 for sure, possibly 2/4, and Gen 6 /definitely/ takes place after Gen V.
So, I'm gonna say chronology is this:
>Prime Continuity
1. R/B/Y/R/S/E
2. G/S/C/D/P/P
3. BW/B2W2
4. XY
>Modified Continuity
1. B/W
2,3,4 FR/LG/B2/W2/X/Y/
5/6. HG*/SS*/OR/AS
7. (GEN IV REMAKES) (starts midway into HG/SS, as with D/P/P)
It makes sense that OR/AS takes place after X/Y because suddenly Mega evolution is a big damn deal, and you can sure as hell bet that if a shiny gyarados in Johto makes the news in Sinnoh, a fucking supervillain attempt to eradicate life in Kalos would definitely spread worldwide, and with it all the other stuff that is going on in that region.
Steven Stone gets interested, starts poking around and mega evolution knowledge is brought to Hoenn. Birch is studying pokemon evolutions, makes sense that he and Steven would compare at least one or two notes.
I put B/W first in the second one, but really I'd imagine it starting at roughly the same time as FR/LG, because of the complete absence of Oak. He's busy in Kanto and can't be assed to travel to Unova, unlike all other regions, except Kalos, where he is absent for the same reason.
Hell yes, I did just overthink this.
*only issue is the lack of fairy typing