as the protagonist is studying with the professor who studies evolutions, what better pokemon for him than some of hisui's old evolutions? that I must remember, is the old Sinoh
He should get a Happiny! It can heal his Pokémon on the go and learn gravity to help train his other Pokémon under its effects to strengthen them faster! It could also be given to him by nurse Joy as an egg to show here application for his help!
He left for 5 and a half years and never came back? Seriously? That's not very real or coherent from where you see it, he should return once a month or every 2 months, or every 6 or 1 year, since what happens if the pokemon forget?