Pokemon, what happened to you?

[Chaoxys]

4 starts during 2, as the Red Gyarados problem begins.

I thought that too, but Lake of Rage has a ton of Gyarados in it, and since red Gyarados is his shiny color, it could just be another one. If anything, 2 is a little after 4 because I remember reading somewhere that in HG/SS's Arceus event, you see Cynthia and she states that she was the Pokemon champion. If this is true then that means that it would take place a bit after 4.

this is not likely at all, if cynthia states she was champion then it would be BEFORE 4 since you become champ AFTER that. and another red gyarados? thats just dumb, the red gyarados got his color because team rocket used a radio signal that alternated his color, seeing a simple shiny and not referencing that (along with the other shitload of gen 2 references in dppt) would be silly.

sinnoh is the last region as of right now in terms of ingame timeline.

Yes, she WAS champion, but then she was defeated, so it would be after 4. Also, how is another red Gyarados dumb? Look at the freakin sprite sheets, that is his shiny color which means there can be more than one, the fact that the one team rocket evolved was red was nothing more that a coincidence or side effect that made it shiny.