Somewhat offtopic, but this seemed suspicious to me at the time.
Far from being the disinterested administrative AI that you would expect, Alvis was directly manipulating events and even Shulk into the desired outcome. Shulk even calls him out on it - "It sounds like you don't trust me - I'm supposed to be the God!" (or something like that).
In the scene just before, Shulk's friends all deliver a lecture to him about how it is that people should live, except they weren't Shulk's friends, they were a simulation by Alvis, constructs formed from Shulk's memories. In fact no time elapses from the death blow delivered to Zanza and the creation of the new universe - Shulk's friends stand motionless in the background, almost leaving an open question that maybe the universe had already ended with the death of its two creators. Which has all sorts of other unsettling implications for the new world (in that, for example, that's not really Dunban over there anymore, just a recreation).
Considering that a theme of the game was about free-will vs. determinism, with Shulk being the inversion of the typical hero in this type of story (in that, yes, he is destined and prophesised, but victory requires him to reject his destiny and avert prophecy), Alvis basically manipulating him into making him a colossal decision (and that decision to be that humans should be able exist without fate) is just.. Weird.
I felt like Alvis was following a programming directive to continue experimenting, to continue evolving the world in an endless transition with no stable point. He certainly didn't have any moral objections when Zanza decided to try to destroy the Mechonis - it was specifically the continual reset of life that seemed to bother the dude.
Then I played 2 and thought nothing of it.
Maybe the dissonance was just in my mind, or even if it wasn't, it was just something that didn't occur to the writers.
But 3 already has me recontextualising 1 and 2.
Xenoblade is a pretty fun take on determinism vs free will, as it starts with a determined world, as a story literally written by an in game author, and then injects a free willed agent of chaos into it. Like imagine there is a play running, it has to go on, but some random asshole got in back stage and keeps running out on stage and doing shit. Like say a character is supposed to tragically die to a monster but he runs on stage and saves him. Now he's alive, and still there for all the rest of the acts where he has no part written..... Now he's a free willed asshole doing whatever he wants on set. The impact of the act ripples out. Butterfly effect.
Manipulating shulk seemed to be a national past time of the bionis/mechonis universe.
Zanzas entire plan, his pre established harmony of events, was a big horse and pony heroes journey show to manipulate shulk, his next vessel (and as such one of the only beings with free will potential in the universe) into following his plan of his own free will. Alvis, was trying to manipulate him into defeating zanza, and making a new universe, and even Meyneth, specifically chose Fioras body for her vessel, in order to manipulate shulk into choosing the direction away from zanza.
Alvis was definitely pretty sus. Definitely leaned further into that hal 9000 inspiration than any of Takahashi's other ai's before blade.
They established pretty early on that he was capable of straight up lying and deception. Well before they established front and center that he was an ai.
And they also established he can't really do much of anything Monado wise unless a user issues a command for him to execute. He is very.... Prompty. Which definitely feels following programmingy. He seems to stretch as much as possible the interpretations of his programming, but still ultimately seems bound by it. So indirect, manipulation is pretty much his main game.
I'm not sure what kind of morality a being like alvis would have, or how he would express it, my guess is functional rather than emotional, but he does seem to be following the Monadologys law of sufficient reason from a big picture standpoint.
Say, if he did take issue with zanza deciding to destroy the mechonis? What would he do about it? He seems restricted from disobeying zanzas commands as a user and simply not executing them. So he would need another user to counter him, and make the commands he wants/needs to achieve his goal, hopefully by finding a user who shares the same goals.
We know of 3 users or, as I guess they have been dubbed now:
Drivers to Alvis during this story. They are the exact same number of beings who are capable of existing outside the pre established harmony of events. All Monado users come through Alvis.
Zanza, Meyneth, and Shulk.
we actually know quite a lot about the commands both zanza and Shulk made through Alvis. We know basically nothing about Meneyths relationship with alvis. In fact the lack of information is such a complete black hole, that if we didn't know every Monado user (as opposed to beings used by the monado, like Arglas and Dunban) has a direct relationship with alvis, the Monado, we would be led to believe these two never came into contact or ever had anything to do with one another.
Zanza obviously isn't going to make the commands Alvis wants to execute. But he can not directly disobey him.
Meyneth seems like she definitely would make the kind of commands Alvis would prefer,
or already did/was. However, due to her refusing to consume her creations to repower and revitalize herself, defeating/stalemating Zanza resulted in her going out of commission and into hibernation. So she wasn't on the playing field for the time being, and even if she were, she might not be enough.
when zanza went into hibernation, he set into motion a plan, what he called a pre established harmony of events. In reality he wrote and had alvis execute an overwrought, overcomplicated, program script that encompassed the mechonis, bionis, and all the beings on it, to deliver his new vessel, shulk, and set up a show that would get his vessel (who could not be directly programmed like other beings) prepared, so he can take, and use it to continue his existance.
We do not know what Meyneth did before she went into slumber. But she sure as shoot seemed to have a plan in place the moment she came back. She was very quickly up to speed on what Egil was doing, had an inside woman ready, and took advantage of his face mechon program to specifically aquire fioras body for her host, whom she already knew was close to zanzas chosen vessel. So maybe she's really fast on the uptake, or maybe she has access to a technology that can run simulations covering long periods of time that can be so accurate they can be seen as visions of the future..... Regaurdless, she hit the ground running when she came back, and quickly threw a massive wrench in zanzas delicate pre established harmony machinery, majorly over clocking shulks butterfly effect rampage to more of a.... Bull in a china shop effect.
So yeah, there was a lot of shulk manipulation going on.
if you want to get into some really uncomfortable mind slips with this story, think of Fiora and shulks relationship before Fiora gained free will.
everyone in the universe was part of a script for shulk, so Fiora was actually zanza (everyone was besides shulk and characters like Dickson, who while knowing what was going on, didn't exactly have free will in a different way). Every heart to heart about past events, like talking about getting married, and the sandwich scene, was zanza. He wrote the script.
Upon escaping the pre established harmony of events, the fake relationship between shulk and Fiora, something entirely scripted by zanza, is never thought about, or examined by either of them, they just keep on going with it.