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.
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, ie. reality incarnate. There's no way guys like them would fall to those simple Mooks.
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.