I never even realized it's supposed to be implied the protagonist has amnesia. Is that really the case? If so Arceus is a completely evil and lazy bastard who kidnaps trainers with successful careers and lives and throws them hundreds of years into the past while also erasing their memories so they don't go crazy/become distracted/refuse to help in order to fix things that he could probably do himself but doesn't want to because he is too tired and is preoccupied thinking of what to eat for his next meal and then he never even bothers to return you back to your time and home after you finish, probably thinking it's better if you stay there to keep things in check or maybe because he's still too tired and doesn't want to use up a lot of energy to open up another time portal. Arceus probably pulled Ingo from Unova, forgot what the next step of his plan was, left to try and remember, comes back but forgot where he left Ingo, pulls another trainer. Given the age discrepancy, he targets randomly as long as they have powerful Pokemon with them. Also, another theory as to why Ingo got left behind is when Arceus returned to the present time he saw Emmet and thought it was the same guy he pulled earlier and left it at that thinking the time loop/warp/paradox fixed itself. It's some kind of curse of the Pokemon world, any human who become too powerful of a Pokemon trainers runs the risk of being noticed by Arceus and having your life essentially destroyed as you know it.
