The Nopon terms for High Entia and Telethia ("bird-people" and "dino-beast," respectively) are surprisingly meaningful once you discover how the two are related. After all, didn't birds evolve from certain species of dinosaurs?
After The Reveal, it makes a lot more sense why The Monado can't hurt Faced Mechon. The Monado can't hurt Homs, and Faced Mechon ARE Homs.
There is even a conversation with Linada that says that the red lines on Faced Mechon are tubes pumping the Homs' blood though it.
Shulk's Heroic RRoD on the way to the Mechonis Core happens not long after he tries to make the case to Egil that Mechonis and Bionis can live in peace. I guess Zanza really didn't appreciate Shulk going Off the Rails of his grand plot to destroy Mechonis.
Also note that the Apocrypha Generator was still active at the time. It's possible that Zanza was trying to kill and/or possess Shulk at that point, like he did with the Monado's previous wielders, and it was only because the Monado's power was suppressed that Shulk survived more-or-less intact.
Guest Star Party Members Dickson and Alvis are effectively unbeatable when they fight alongside you, their HP never droping below one. That's kind of silly until you figure out their true identities. Dickson is Zanza's disciple, granted with immortality; and Alvis is Monado, i.e., reality incarnate. There's no way guys like them would fall to those simple Mooks.
Likewise, the Hopeless Boss Fight with Zanza also has Fiora equipped with the Unbeatable IV gem, like the 2 above. She has Meyneth inside her body, who's a God herself, and could stand toe-to-toe with Zanza.
Also in the sequel, this is one of Pneuma's many special abilities, making the similarities between her and Alvis quite close, implying Alvis is Ontos.
While there is a canon explanation (that is All There in the Manual) for Fiora getting her old Homs body back (there's a machine that can regenerate her body, that they used after her upgraded abilities were no longer needed), there's a plenty plausible reason for it even without that. At the end of the game, however briefly, Shulk is basically god. If there was one thing he'd want to do with that power, wouldn't giving Fiora her body back be right on the top of the list?
A minor one, but the icons for Landmarks on the map are monoliths.
Early in the game, it is established that falling debris is a common problem for Colony 9. Then, after one debris alarm, this is never brought up again. It occurred to me that there was a very good reason for this - On Bionis' leg is Colony 6, which had frequent altercations with Mechon. The one time the debris alarm is brought up is the day before the Mechon attack on Colony 9, when the Mechon assault on Colony 6 was drawing to a close. The debris that keeps falling into Colony 9 airspace? Wreckage from the battle, both Mechon and Homs machinery alike. The reason it stops? Because the battle for Colony 6 came to a close.
During the cutscene that take place in outer space shortly after Zanza emerges from Shulk's body, you can see numerous features of our own solar system, such as planets and asteroids. The presence of these things makes a lot more sense after you learn that the universe of Bionis and Mechonis was created right after the old universe (the one in which we live) was destroyed, so the features in our solar system, just like Shulk's mortal consciousness, were never supposed to belong in the new universe in the first place.
The places where the two important races in Xenoblade- Machina and Homs- were created from on the Bionis and Mechonis reflect their hosts opinions of them. The Homs come from the feet of the Bionis, representing how Zanza feels little for them, like they should grovel at his feet while the Mechon and Machina come from the Mechonis's chest, representing how Meyneth loved them (seeing how the heart is usually located in your chest, and that's said to be the "love" organ).
Why does White Eduardo only show up during thunderstorms? Albinos tend to sunburn pretty easily, and Brogs are (seemingly) amphibians at that.
Gem crafting reveals that as a shooter, Riki's the best at making Gentle flames while the worst at everything else. Actually using him for gem crafting reveals that Riki uses his normal arms instead of his wings in order to fiddle with the gem furnace. Riki can't reach the valves in order to make the flames any hotter due to him being the shortest playable character in the game.
One may be wondering why someone as old as a Nopon Sage would have the voice of a Nopon child. While his age can be excused by the fact that he's seemingly magical, defeating the Unreliable Rezno, a mythical monster only previously beaten by the Nopon Sage himself, reveals that the monster is apparently the source of the Ocean Elixir of Life. In other words, the Nopon Sage, himself, had subjugated into a permanent Fountain of Youth in order to survive as long as he does today, with the side effect of regressing back into the form of a child.
The track "You Will Know Our Names" usually plays against Unique Monsters, but it also plays during two storyline boss fights (instead of the usual "One Who Gets In Our Way"), against Metal Face and against Dickson, both on Prison Island at that. And incidentally, both of them are Dunban's former war comrades turned traitors. You will know their names indeed.
Bonus points for both battles taking place in the same location.
Egil's Gold Face Mechon is named Yaldabaoth. This seems like a random name until you progress further into the story. Yaldabaoth in Gnostic mythology is an arrogant solar deity who suffers from a complex of cosmic egotism and falsely believes himself to be the only god in the entire cosmos. Sounds like a certain Zanza that Egil wishes to destroy. In naming his Mechon Yaldabaoth, Egil mocked the fuck out of Zanza to boot. Also worth pointing out is that Gold Face has a tail; while unusual, it represents the Gnostic Yaldabaoth, who is a serpent.
It seems unlikely that no person ever discovered the fact that High Entia spontaneously mutate into Telethia when exposed to large amounts of ether. For one, it seems to be very easy to just accidentally turn into one if that were the case. However, given that there are still Telethia flying around Bionis without Zanza's presence indicates the possibility that some DID turn into Telethia and the ones still remaining are just mutated High Entia. After all, it is implied that previous High Entia rulers did know about this and tried to keep it a secret.
The fact that you need a lot of ether to turn High Entia into Telethia doesn't make much sense when you consider the fact that Zanza requires a large amount of energy to be reborn. But one of the first things you hear about Telethia is that they absorb large amounts of ether from their surroundings. Their main function seems to be to gather the ether for Zanza, in addition to being used to kill uncooperative sentient life.
Fiora, upon being given a machina body, is being inhabited by Meyneth, the soul of Mechonis and a god, seemingly out of nowhere. So, this is a literal case of Deus ExMachina.
After beating the game, watch the opening cutscenes again. First, in the battle of the titans, the Mechonis is mainly defending from the Bionis' attacks. Second, Dickson's remarks that "you can't talk reason into a beast" [Dunban] take on a darker tone.
The life on both titans reflects the very nature of the two gods. The Bionis is filled with creatures that need to kill each other to survive, forcing a survival of the fittest mindset that is meant to keep life bound to Zanza. Gathering ether also requires people to dig into the very titan to collect it and go into mines, where monsters await to fight and kill them. The Mechonis is free of hostile lifeforms that could threaten the Machina, who are able to gather ether easily from the floating devices Meyneth built for them to collect it from. Likewise the dangers of living in a giant machine are somewhat negated due to child Machina residing in floating devices that are part of their bodies until they reach adulthood, preventing them from falling into the toxic ether found at the bottom. What monsters that do exist in the Mechonis are the Mechon, which were built originally to protect and help the Machina.
One other thing also stands out... so when Galea became Meyneth, the people Mechonis created were the Machina. Seems weird, I guess that god had a thing for machines, huh? in Xenoblade 2, Klaus explains aspects of that scene where the universe was created that we didn't get to see... that Klaus told Galea that humans weren't so bad after all. Apparently, this person may have thought Humans Are Bastards, and Klaus tried to mention it. So who's to say that the Machina are what Galea, also known as Meyneth, aren't her own idealised vision of what humanity could become?
Shortly after arriving on the Fallen Arm, Fiora is incapacitated and requires a piezoelectric unit to continue functioning independently. You find this particular item around the wreckage of a Faced Mechon. Who's to say it wasn't Mumkhar's?
The scene at Prison Island where Metal Face "kills" Zanza may not be as much of an example of Evil vs. Evil example in hindsight. Metal Face didn't kill Zanza, he killed Arglas, so it can still count as one of Metal Face's many atrocities.
All Faced Mechon seem to have 3 names: the name of their Core Unit (the one controlling them), a name indicative of their armor color, and their actual model name. Egil, Fiora, and Xord; Gold Face, Silver Face, and Bronze Face; Yaldabaoth, Face Nemesis, and well, we don't learn Xord's model name—at least not immediately. It's a clever way to hide the name of a late game enemy: the Mass-Produced Faces. It's also a way to hide the fact that Xord is really just an Elite Mook, apparently being so good at wielding his hammer because he used to be a blacksmith.
By the end of the game, there are three major factions: the heroes and their allies, the Mechon, and the Bionite Order. All three get representation in the prologue. Within your team, no less.
Three is a holy number and the game loves to reference it. The gods all have a trinity halo-pattern somewhere in their design. For Meyneth, it's around her body. For Zanza, it's three halos circling a central one above his head. Alvis has it on his back jacket. But who else has halos on his body? Shulk's red vest, indicating his ascent into godhood as Zanza's Soul Jar.
After the initial Mechon attack and Fiora's death, Shulk and Reyn converse about what to do from then on out. Shulk comments that there's another voice in his head telling him to "destroy the Mechon, every last one of them" and that Reyn would think it's unlike him. After you realize he's housing Zanza's soul, it's entirely possible that wasn't all Shulk.
All of Fiora's initial arts are either copied from Dunban (Butterfly Step and Lacerate having similar features to Blossom Dance and Gale Slash) or synergise with Dunban's arts and role on the team (Screw Edge allows Dunban to set up a Topple without needing to use Electric Gutbuster, Hidden Thorn can Daze a Toppled enemy, and Power Smash gains power when used from behind, while Dunban draws the aggro). In addition, one of Fiora's best Skill Links, Critical Drain, comes from Dunban. Her big brother acts as a large influence on her fighting style gameplay-wise.
A bit of hindsight that occurs from Xenoblade Chronicles 2, in that the sequel revolves around the magical Blades and their Drivers that wield them. Given the revelations in both games, it's clear that by all means the True Monado and Alvis himself are at least implied to be one of the three Aegis Blades, which makes Shulk and previous Monado wielders Drivers. Thus all of Alvis' appearances despite being part of the Monado make sense in hindsight, given that it's exactly how Blades can function.
At first, Shulk coming back to life after Zanza leaves his body might not make much sense, given that Zanza was the sole life force of Shulk. However, after playing Xenoblade 2, it's evident that Alvis is the one who allows Shulk to keep living. As he is the missing Aegis, Ontos, he split his Core Crystal in half and placed it on Shulk's heart, thus giving him the life force necessary to come back from the dead. The only reason you don't see it is because the crystal is hidden underneath his clothes.
Additionally, it makes sense that Alvis's Aegis Weapon only manifests itself at the very end of the game. As he is the one that maintains the reality of the Xenoblade world, it is quite possible he does not have the power to summon it normally. It is also implied that the Mechonis and Bionis Monadoes are created because Zanza and Meyneth draw power from Ontos himself. During the final battle, Shulk is in close enough proximity to both Monadoes that Alvis is able to remove the borrowed power from both Monadoes and summon his Aegis Weapon, the TRUE Monado.
Much much later in Xenoblade, the player witnesses a scene in which we see the birth of the universe. The same scene plalys in Xenoblade Chronicles 2 - but it's not a one-to-one remake. In Chronicles 2, we see Klaus calmly explaining his reasons for creating a new universe. But in Chronicles, Klaus is depicted in a much more sinister light and even throws Meyneth to the ground. So why is the scene in Chronicles 2 different from Chronicles? Two words: Unreliable Narrator. In Chronicles, we're seeing the scene from Meyneth, Zanza, or Alvis's perspective which had every reason to depict Klaus in a much more negative light. Whereas in 2, we're seeing it from Klaus's perspective - in which he is justifying his actions and mentions he thinks what he's doing is right.
One of Shulk's first visions shows the Arachno Queen impaling and killing Reyn in one blow. If it weren't for Monado Shield kicking in just in time, Shulk would have lost both of his best friends within days of one another.
Three times, if you count the vision he gets when putting the Monado back before the attack.
Another one of his visions involve Otharon pulling a Heroic Sacrifice to stop Xord. Except that in reality, it turns out that Xord would have survived that. Had Shulk not defied that vision, Otharon would have died for nothing.
It's possible that the entire Ministry of Research is working, knowingly or not, for Zanza and/ or the Bionite Order. Lorithia is the head of the Ministry of Research, and we see her in a room with Telethia in tanks in a cut scene. You also hear from Jer'ell about rumors that they're doing inhumane experiments while she's in Alcamoth.
In addition, Kallian states that the Havres units, the flying vehicles the High Entia bring to Sword Valley, were created by Lorithia and her Ministry. In all likelihood, the Havres were purposefully designed to overload their pilots with ether on command, turning the pure High Entia that were riding in them into Telethia.
During the kingpin quest chain, Dedeba is arrested by the Alcamoth guards for the unlawful distribution of Highmore Caviar. You never see him again in this playthrough, so it is presumed that he is locked away for the remainder of the game. Now fast forward to the events follwoing Mechonis Core. The majority of Alcamoth's citizens are either turned into Telethia or killed in the chaos following, with only however many half-High Entia could fit into the transports escaping. Assuming Dedeba was still locked up, that would put him directly in the middle of that mess.