Noishe, while only IDed as a "dog" or "protozoa" in game, quite clearly fits the description of a Cu Sith (pronounced "coo shee" of Scottish Mythology. In case you don't get it, it's supposed to rhyme (the English version of the game screwed it up.).
The end sequence music is the same tune used in the end sequence of Tales of Phantasia. This also happens with one of the battle themes as well. Fighting of the Spirit plays in this game and it's sequel Tales of Phantasia whenever you fight a summon spirit.
When you go to the night-time area of Altamira, you can see a stage play being performed by the Katz. For people who didn't get the joke, Cats is an Andrew Lloyd Webber musical.
The placement of the skits - the ones where you can choose a response which might affect your relationship with the character - seems to be mostly random. But the two skits outside Flanoir make so much sense. The two skits are with Zelos and Kratos. Flanoir is where you make the decision between keeping Zelos and or inviting Kratos back into your party. Kratos's skit is one where you must choose whether to talk to him or ignore him. That's the exact decision you make in Flanoir to keep him or not. In Zelos's skit, if you pick the positive response, Lloyd observes that Zelos is brooding more than usual, and Zelos seems really surprised by the fact that Lloyd might actually care. In Flanoir, Lloyd saying either "I trust you" or "I want you to live too, Zelos" - showing Zelos that he does care - is pretty much what keeps Zelos from committing Suicide by Cop. Additionally, Zelos more or less admits during the Flanoir scene that the snow reminds him of his mother's death. Perhaps that's why he's brooding outside Flanoir?
Considering how familiar Zelos was with Kratos and his motivations, as well as Zelos's heavy involvement with Cruxis it's entirely possible that the reason they have nearly identical fighting styles is because Kratos might've trained him at some point.
The Seal of Fire is said to be made out of polycarbonate, which can only really be made by our level of technology, as it's a type of plastic. It's the first hint that the Medieval Stasis game isn't just a setting trope. Another interesting hint comes from the rather futuristic teleporters that can be seen in the Renegade bases, the seal temples, and the Desian bases (and later the Tower of Salvation and Welgaia). At first glance, it appears to be a regular dungeon gameplay trope, but on closer inspection, its probably because the three groups have the same leaders and thus the same access to magitechnology.
At the beginning of the game, you can only buy gels that restore 30% of HP or TP. You can only start to buy the ones that restore 60% when you reach Meltokio. Why is this? Because gels restore life force and magic- basically, the body's mana. It's not unreasonable to assume that gels are made of or with mana. Sylvarant doesn't have enough mana to mass-produce these products! To add to that, there is actually one place in Sylvarant where 60%-restoring gels are available- Katz Island, which is only reachable after you've released all the seals and evened out the mana distribution a little. (Nobody but the Katz dared try to waste precious mana on creating so many things, as most people cannot sense subtle shifts in the mana flow. Also, if all of this is actually true within the setting, that means that the Katz could secretly be elves or half-elves.
Mithos' final form at the end of the game seems like a Giant Space Flea from Nowhere (especially since it just appears without a word from anyone,) but makes a little more sense if you remember the three boss fights preceding it representing the personal demons and Fatal Flaws of Lloyd's comrades, of which the final form is a fusion of all three. His personal demons have basically consumed him.
When you first visit the Tower of Salvation, the party is horrified by all the coffins in the entry room of the Tower. Raine even theorizes that this is where all the bodies of the failed Chosens are kept. Fast forward to later in the game, if you end with the path where Zelos performs a Suicide by Cop, with the claim his entire life was a mistake - guess where it all goes down.
More like "Fridge Tearjerker/Depressing", but...the cutscene where Yuan loses his engagement ring is mandatory. The sidequest where you return it is not. So presumably, if you don't do the sidequest, he still retraces his steps searching frantically for his precious keepsake, and never does manage to learn of its fate. Poor guy.
Kratos thought that Lloyd died as a child, falling off the side of the cliff with Anna. This means Kratos and Dirk never actually met, and that all of Dirk's information about Lloyd came from his mother. This means that Anna must have communicated to Dirk from within the Angelus Exphere. Dirk knew all along that Expheres are actually Soul Jars. It sheds a new light on Lloyd's ability to carve Key Crests.
In the manga version of Zelos' backstory, when his mother is killed, the manga seems to draw it so it looks like his mother is Taking the Bullet for him. If you didn't already know what she was going to say next, this makes her Famous Last Words even more shocking and horrifying than they already were, since it looks like she's taken the bullet for Zelos, only for her to suddenly tell him "You should never have been born". THAT'S the Fridge Horror. The Brilliance is that, while Zelos' mother is saying her last words, she's smiling, although it's not a very pleasant one. It appears Zelos wasn't the only Stepford Smiler in the family...
Perhaps I'm looking into it too much but I thought that her face looked really sad when she said it. This makes me think that, when she said he shouldn't be born, she meant "if you weren't born, you and I wouldn't be in this mess and we would both be happier". It's still a cruel thing to say but I feel like she said it more out of despair than out of spite.