Aggron would take on Xerneas while Tyranitar takes on Yveltal, being the perfect counters for each version's legendaries.Honestly Lysandre needed two different teams depending on the versions. He can keep Pyroar, but I think his Mega Pokemon should have either been Mega Aggron (X) & Mega Tyranitar (Y). Then after that either have neutral Pokemon which could work with either Legends (such as Florges) or Pokemon super effective/resistant to the Legendary.
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