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I know that it seems like more Charizard X cocksucking, and while to some degree it is, I think that there is another reason why Steven has Charizard X....
Firstly, look how Charizard X's level is 100.... why would he just be walking around with a level 100 mega pokemon, when that is higher than all other NPC's in the main game?
Secondly, the battle takes place in a field/route, not the champion's room....
So because of that I think that the reason Steven "has" Charizard X is a postgame encounter, where he will give you one of the old megastones once a day or so, if you can beat a level 100 of that mega.... That would allow him to still have mega metagross, and charizard X. Also gives you the postgame that X/Y lacked