I am curious to know what is everyone's head-canon playthrough throughout the series?
I have two different continuities.
1st and 2nd Gen are their own Continuity.
Red is the protagonist from 1st Gen and uses the team he has when you face him in 2nd Gen and does all of the events from that game. My character starts off in Johto(Crystal Version) and does the main events from that game all the way up to Red his story ends there. Stadium is not canon, did not complete pokedex.
Main Team: Typhlosion, Pidgeot, Suicune, Dragonite, Espeon.
The Modern Continunity:
3rd Gen: Kanto is pretty much the same as 1st Gen Kanto except with the Sevii Islands and Stuff. Hoenn's events happen as well but My character is not seen just yet. Colosseum( XD doesn't happen until 5 years later.....so its non-canon in my book for now)'s events happen. Wes gives the Purified Shadow pokemon away to drift(Im debating if I want to include Espeon and Umbreon but that wouldn't seem "in character" y' know?.)
4th Gen: Johto(Soul Silver) is where my Main Character Starts. Does all the events in game up to beating Lance. Becomes champion.
Team at that point: Typhlosion, Pidgeot, Vaporeon, Ampharos, Dratini(not trained) with Red Gyrados and Scyther(National park) as his extra Pokeatholon teammates.
Before his tour of Kanto, he goes to Sinnoh(Diamond). Does all of the events there up to the Stark Mountain.
Team at that point: Infernape, Luxray, Floatzel, Honchkrow, Riolu(never trained just hatched).
Come back home to Johto, integrates Honchkrow and Riolu into the main team. Does the Kanto part of Soul Silver culminating to the defeat of Red and All of the Frontier Brains. Gets Charmander from Oak and Mudkip from Steven.
Team at that point: Typhlosion, Ampharos, Vaporeon, Honchkrow/Pidgeot, Lucario, Dragonite(Extremespeed)
Now this is where things gets tricky. Goes to Hoenn with the Mudkip given by Steven and does every non-plot related event in Hoenn(Team Magma and Team Aqua, Norman as dad, etc.) becomes Champ, beats Steven in meteor falls does not compete in Hoenn's battle frontier.
Team at that point: Swampert, Gardevior, Breloom, Swellow, Ninetales
Decides to see what Orre is all about and circuits the Colosseums(Think Battle Mode not Story Mode. Finds Wes. Adopts the Purified Shadow Pokemon. Uses a couple of them them plus all non-4th Gen pokes obtained in Circuit(Just so it would seem mirror how I played Colosseum)
Pokemon used: Main Johto/Kanto Team, Hoenn Team, A few of the shadow pokes(Suicune and Hitmontop more than most), Charizard
5th Gen: The Events of Black happen without My Main Character. Two years later after the events of Black, My main character arrives to Unova, does all of the events up to the PWT which he is currently participating in. (XD's Events could happen here but idk yet.)
Team Used in 5th Gen prior to PWT: Serperior, Lucario(new one), Flareon, Flygon, Swanna, Galvantula
PWT Team: Typhlosion, Vaporeon, Serperior, Dragonite, Honchkrow, Lucario. Subs: Breloom, Galvantula, Ampharos, Swellow, Suicune, Hitmontop.
And that's pretty much it.