You'd think AZ getting the box legends to power his machine would have come up more than like one line of dialog in the post game (I will assume that surely there is at least one more line and it's jsut not as easily searchable, perhaps its in the flare base files)
The only thing that the files in the lab have to say about them is literally just a rephrased bit of Mable’s dialogue from XY
“Kalos is said to have two Legendary Pokémon. Xerneas—which represents life and rebirth. And Yveltal—representing destruction and death. The power to grant life and the power to steal life. These are mysterious abilities that even science has not been able to decode. What would happen to the world if we were to use such power to activate the ultimate weapon?”
I suppose if you read very,
very deep between the lines and cross this with Mable saying during the Project M side mission that Team Flare considered using Mewtwo to power the weapon, but decided not to since they couldn’t get it to
do anything but stand around Mega Evolve, and the fact that Mega Evolution itself is derived from the power of Xerneas/Yveltal, that
maybe Xerneas and Yveltal’s stores of life energy are somehow unique in a way that enables the machine to function in the way that we’re familiar with… but it’s also never been clear if AZ needed (both or only one of?) the Legendaries in order to facilitate the life energy transfer to Floette, or if he just used them as batteries for the giant laser blast. Ange doesn’t seem to require them at all since Lysandre deemed it useless without Eternal Floette despite having control of Xerneas and Yveltal, but I guess it’s possible that
if they were indeed used to enable the resurrection process, then Floette may have derived some key trace of energy from them herself.
And in any case, “the device very specifically requires them in order to function because of their unique life/death powers” wouldn’t be much of a solution to the larger issue you identified. It’d just be saying that you can’t wilfully manipulate their energies without a very specific and convoluted kind of mechanical interface, like the Blue/Red Orbs or the Red Chain x50. I think to do anything significantly more satisfying with them would probably require some extremely substantial rewrites to the story. Rewrites to a degree of substance that I doubt even the planned Z games would have pursued.
On top of that lack of distinction, AZ didn't even get eternal life from the life giving version of the weapon, he got it from the killing version
Which is yet another thing I could easily see coming from a different sort of series or narrative style — “the thing I used to bring untold death and destruction cursed me with eternal life” — but is not something I’d have really ever put my chips on Pokémon doing. It’s very poetic and ironic, like a Greek tragedy almost. Personally, I love that Pokémon went for something like that, but it’s operating on a notion of narrative karma that’s a lot more complex than “Bad guy seizes power and gets more than he bargained for, and his plans are foiled.”
Even disregarding what Z-A brought to the table, I think a concept like the ultimate weapon is just so much more semiotically dense than an ancient superpowered creature. Groudon, Dialga, and Zekrom are all just natural facets of the world that Pokémon takes place in. They’re the fantasy of “What if we could own cats that shoot lightning?” taken to its most logical extreme — “What if we could own cats could shoot so much lightning that they could fry the whole world?”
But the ultimate weapon has a material context and analogy that we can map directly onto the real world. The horrors of human warfare produce horrifying weapons made by human hands, often by perverting the miracle of science toward the aim of cruelty and harm, and later generations will inevitably inherit the legacy of those weapons and thus must bear the burden of figuring out how to navigate such a great responsibility.
You could certainly make it so that Team Flare just want to capture Yveltal and force it to suck out the life force of everyone outside their group. After all, the outline of their plan is essentially no different from what Cyrus purported Team Galactic’s plan to be; they want to create a world just for themselves, just without all the multidimensional trappings. But that would ultimately just be another story about a man trying and failing to control a force of nature and being humbled by it. Whereas XY as it is, is about a man who has lost faith in the world choosing to perpetuate a terrible genocide that was carried out once before by using a weapon his ancestor created to achieve a Pyrrhic victory.
Again, I do enjoy this for what it is, but how the hell did Pokémon get here? Was Masuda just on some high pretention shit in 2013?
To your point about it feeling like you could excise Xerneas and Yveltal from the script altogether and nothing would change, it almost makes me wonder if they exist mostly for the sake of adhering to some tradition, and perhaps that’s why their lore is so shallow.
“We’re doing two versions, so we need two diametrically opposed mascots.” = “Well, life and death are a theme of the story, so maybe life and death Pokémon.”
“We always have the Legendary show up to be caught during the climax” = “Maybe in order to justify having Xerneas / Yveltal there, we say they’re needed to power the weapon.”
Not to connect too many dots, but I also recall Sugimori saying that he had difficulty coming up with a design concept for them.
I wonder if in hindsight they wished they’d thought of taking a Nebby-type swing one generation earlier. Just have the weapon be its own inanimate menace and have Shauna carry around a Zygarde Core like Bonnie in the anime. Don’t even have Xerneas/Yveltal exist (I wouldn’t
actually want that; I love their designs, but for the sake of the hypothetical), just give Zygarde two forms or evolutions or whatever and have “life” and “death” be abstract, unpersonified forces that Zygarde keeps in balance.