*crazy theory incoming*
Hood Man is Mewtu obviously. Sird escaped to Unova after FR/LG to visit her secret hideout full of secret armors. She used one to trap Mewtu inside and to restrain his power just like Giovanni did in FR/LG. Mewtu can't fly anymore so Sird could easily escape to Sinnoh. But Mewtu searched in Unova for trainers who are
2) strong enough to break the armor.
Because of his past Mewtu refuses to go to a human lab. (and trust som random scientist) to remove the armor. But it challenged the gym leaders to get in contact with the elite four / champ. It want to find trainers like the Pokedex Holders. That is the reason for him to be at the pokemon league. Of course it is odd for a pokemon like Mewtu to play the role of a trainer and fight with other pokemon against gym leaders but what else should he do?
Sadly it won't be able to get rid of armor until B2W2 because of genesects real appereance. The armor will be destroyed and all the restrained energy will flow back to mewtus body making it possible to use Psystrike (and beat genesect) Kusaka won't waste the opportunity of a Mewtu Vs. Genesect showdown if he need to use Mewtu's signature move anyway.
So... now I really want something like that to happen ň.ň
Edit: Ups, Mewtu = Mewtwo^^'