No, it is obvious. Ash is actually Ean from Agate Village in the aforementioned Orre Region. Probably some time shenanigans on the part of Celebi and the Legendaries needing his 'help.' (read bitch-servant service) They give him some cryptic message as usual and is sent back in time to guard the Celebi Shrine in the Agate Forest to save the Pokemon and the world or something. Misty either gets sent back with him or she latches on at the last second. They travel the world in the past after a few weeks, because Ash. He becomes a legendary Pokemon trainer part due to his knowledge of Pokemon from the future.
He lady-charms women as he is wont to do. But eventually Misty reveals her feeling for him and they have an on-off relationship until marring. They have Rui, that red-haired girl from Pokemon Coliseum game that can see Aura's and shit. She has her relationship with the protagonist as the story follows in the game. They then go out of Orre to stop the evil machinations of the Evil Organizations that helped/allied with Cipher/Team Snag-em or have a similar agenda. Rui is knocked up. Protagonist dies at the hands of Giovanni, and Rui dies in child labour in Verillian.
This explains Orre ties-in to the story and Red's Orre heritage (Coliseum Protag is from Orre). Also, he has his mother's Aura perception and the inherited his powerful Aura from his Time-traveling Grandfather; you know aside from being super smart. He probably had his Aura corrupted by Shadow Pokemon in his vicinity during conception, and smells like Bug Pokemon due to Celebi's generation-weakened Legendary Taint. So he smells like Bugs and death or something, attracting hungry Bird Pokemon everywhere.
Ash is presumed to be dead in the present, since he was never found. Ash's mom, never got closure without a body to bury. Oak is Oak; he probably met Ash in his Pokemon 4ever Movie and his Legendary Ean counterpart. Gary lost his stupid rival; he hasn't found a rival worth his time since. Silver is Giovanni's son as usual. Green is some boy with a bone to pick with Red. Blue is… Alright not sure on that one; maybe she is a relative of Misty's family or spiritual successor. No one cared for Misty because her parents are dead and her sisters a grade-A bitches. (Well aside from Brock and Delilah. Maybe Gary if he had a crush on her.) Gold is probably pure post-story. Crystal might be out there catching all the Pokemon on every route for professors. Brock was not in the area or knocked unconscious during Celebi's re-appearance and curses himself for losing his two friends.
Throw in some tropes like Ash's slut-ness resulting in Red's half-relatives. (I mean just look at all the one-offs and rival girls/Pokemon that crushed on him during the 20+ seasons supposedly occurring under a year. Imagine an adult him with abs and no shirt while lovingly taking care of his Pokemon.) Yellow maybe?
Trope 2)
Giovanni: "No Red, I am your father's killer."
Trope 3)
Somepony: His Aura is over 9000!
Trope 4)
Red: You'll never get away with it!
Trope 5)
Shadow Lugia: Roar! *Shadow Psycho Boost followed by a Shadow Hyper Beam*
Red: *Shitting his pants and rocking himself back and forth in the fetus position, while his Pokemon both console him and pull him to safety*
/crack-theory
PS: I was not high while writing this, I swear. Just have a hyper-active imagination.
PPS: I like where this is going. Please continue.