>>38346388They have *the Ultimate Weapon.*
AZ was never even implied to have powered it with Xerneas and Yveltal to begin with. He used the stones on Route 10 to capture the life force of massive numbers of other Pokémon. Team Flare is explicitly stated to be doing this as well (there are Grunts blocking both ends of Route 10 talking about this, and Trevor and Tierno explain that that's what they were fighting during the climax). They don't NEED Yveltal because they already *have* the Ultimate Weapon.
Of course, it's also quite badly explained why they need either mascot. The Ultimate Weapon was also capable of restoring life. I think Xerneas at least makes a little more sense - AZ tells us that the "machine" that revived Floette was modified before it became the Ultimate Weapon, so it might no longer be capable of that without AZ's ingenuity to change it back (and he's obviously not willing to help them).
One could say, then, that they *have* everything they need to end all life (with the Ultimate Weapon), and the reason they need Xerneas is so they can make themselves immortal first. That's why they can't do anything until they have it - not because they need it to charge the Ultimate Weapon, but because they need it BEFORE they charge the Ultimate Weapon or they would all just die with everyone else. Yveltal, on the other hand, has remarkably little reason to be relevant because they have no way to give themselves immortality and it's redundant to what they already have.
Of course, the game does an awful job of explaining all of that and I think even my own explanation contradicts the way they actually say Xerneas is being used. And I'm pretty sure Lysandre says in BOTH versions that the Ultimate Weapon is going to immortalize Team Flare AND eliminate everyone else, but never what the particular mascot he chose has to do with it or why he only needs one.
Game Freak really just had no idea what they were doing with the lore in Gen VI.
