Essentially all of Luke's snappy, over-compensating bluster, difficulty adapting and need for validation during the first section of the game looks very different once you realize that he’s a seven year old child who’s been expected and pushed to act twice his age his whole life.
Arietta's stating that her opponents will fight as a team of four during her Duel to the Death sounds as though she is adhering to the Arbitrary Headcount Limit, but there are exactly four people she has a grudge against; Luke, Tear and Jade for killing the Liger Queen, and Anise for her responsibility for Ion's death. Granted, you don't have to use those four.
The ending to the game leaves a lot of things open-ended, like the new role of the Order of Lorelei, the place of replicas in the world, and the identity of the Luke who returns to meet the others. But that's all part of the game's point that the future isn't set in stone, and there are many possibilities. Starting from that point each player can imagine the world developing in a totally different way.
Lorelei reveals that Van has trapped it to Luke by calling him "The One Who Would Seize Glory" which is the meaning of his name, translated from Ancient Ispanian. Thing is, Lorelei didn't mean to say it that way, it's just that its message was telepathically translated for Luke to understand, so everything ended up being translated, even a person's name.
Fridge Logic: Then why is Luke's name never translated, too?
Because it isn't saying 'Light of the Sacred Flame, find The One Who Would Seize Glory!'. Lorelei sees 'Luke' as a name, but 'Vandeldesca' is more of a word during that exchange to it.
Luke's inferiority complex and angst gets a lot worse during the month long timeskip, this makes perfect sense since he had nothing to do that entire month, so naturally he'd dwell on his insecurities and they'd get a lot worse without anyone to help him.
Ion has no identity or existence outside of being Fon Master, but it's not because he's Married to the Job- it's because he's a replica of the original Ion and is only 2 years old. His entire life so far has probably been one big long epic cram session of everything he'd need to know to be able to be the Fon Master- the structure, history, and practices of the Order of Lorelei, the Daathic Artes, how to read the Score, the names of important people in the Order, important figures from the Order's history including all of the Fon Masters who came before him, geography, important events and figures from Auldrant's history, and the political structures of all current and past nations in Auldrant... On top of learning how to do basic things like speaking, walking, and dressing himself. He has no identity outside his job because he hasn't had a chance to form one. His job is the only thing he's ever known. This probably wasn't intentional, since most other characters outside the main party don't have an existence outside their jobs, but for Ion, it actually enhances his character.
There's a tiny bit of foreshadowing about Guy's past that is so utterly brilliant it deserves to be put here, even if you notice it after you've learned his backstory. All throughout the Fabre mansion are banners with a very Kimlascan-looking symbol on them. It's probably the Duke's symbol, or maybe the King's. Either way, there's a banner above Guy's bed, but it's folded over so the emblem is blocked. It's because he despises Kimlasca and Duke Fabre. What a splendid touch!
Another sneaky bit of Fridge Brilliance for Guy. Remember in Tales of Symphonia, how Kratos and Lloyd being related to each other is foreshadowed by the fact that they both hate tomatoes? There's another piece of food-foreshadowing here. Every person in Tales of the Abyss has an extra ingredient they'll add to their food, if given the option. Guy's is always fish. As anyone who grew up on an island would know, fish is pretty much an island staple. Maybe Guy misses the cuisine from Hod?
How did Dist survive getting hit in the face with a Fragmented End? Enemy Mystic Artes can't kill the target. Dist was reduced to one HP just like the party!
The four Fonon clusters you gather in the Sephiroth correspond to the Second through Fifth fonons, and are gathered in the same ways (Yellow/Earth/Second fonons are broken with Mieu Attack, Green/Wind/Third Fonons are out in the air, Blue/Water/Fourth fonons, you have to battle in an allusion to the conversation about the Fubras River and how water is dangerous, and Red/Fire/Fifth fonons are gathered with Mieu Fire).
You have to complete the entire plotline up until the final battle in order to unlock Peony's last set of costumes. Why? Look at Luke's Wild Saber costume a little closer. He's wearing a shredded part of Asch's clothing, which was presumably taken from his corpse. Somehow.
There's a stealth sequence in the game in which you're trying to avoid fighting the opposing soldiers for fear of causing trouble. If you can't complete the sequence with stealth, the game lets you simply fight your way through... but doing this doesn't harm your cause, because afterwards you find out that someone else is in the area killing the same soldiers. All your killing just gets attributed to someone else, so you face no consequences!
Until much later in the game, nobody really knew Auldrant was a shell floating above the true earth, consisting of a bottomless mudpit and poison miasma. When you go to Akzeriuth, the Miasma starts up...Oh Crap - the miners of Akzeriuth Dug Too Deep.
What exactly is the process of Luke's death? If you think about fonon separation it sounds like he's literally dissolving on a molecular level, but it doesn't seem he's in pain. So either he is and he's keeping very quiet about it, or he isn't, and he slowly falls apart into nothingness without even noticing. I can't decide which idea is more terrifying.
Fridge Brilliance and Fridge Horror: For much of the game, the faction that is trying to egg on a war is doing so because according to the end of the Sixth Fonstone, the war between Kimlasca and Malkuth will bring on prosperity. The entire future of the world, from start to end, is written on seven fonstones. After the war between Kimlasca and Malkuth, there's only one to go. And notice that all the stuff about prosperity never mentions Malkuth. The lost seventh fonstone—the very thing the Order of Lorelei has been working towards for over 2000 years—probably doesn't have prosperity and puppies and rainbows at the end of it.
The Score. According to the game, the Score doesn't just describe world events, it covers aspects of individual people's lives. For instance, people use it to plan their meals. Also, when Luke apologizes to Teodoro for Akzeriuth, he is told not to because it was preordained by the Score. Moreover, it's pretty clear that Auldrant has its fair share of crime. Given the above, what happens if the Score tells someone that he will become a terrorist, a serial killer, a rapist, or a child molester? The person has the choice of becoming a Complete Monster or committing sacrilege by defying the Score (unthinkable in Auldrant). Then, he will either be punished (probably by death) if "The Score made me do it" isn't a defense, or he will go around continuing to commit heinous crimes.
Well... some Scores aren't read. Death Scores aren't. Scores that don't dictate anything other than the above-mentioned puppies and rainbows don't get read to people, unless it can be vaguely implied that the aforementioned puppies and rainbows will come along after the tragedy (such as "prosperity" after a genocidal war). So they become people like that of their own accord which is probably a small comfort because they don't have to choose the path that either way will get them shamed forever. I think the more horrifying part is the victims aren't told, either, because otherwise they'd try to avoid it. People are only told about bad things like that if they're supposed to do something specific in response to the knowledge (such as avoid it, stop the terrorist before he can do anything more than what's dictated in the Score, etc...). "The Score said I would do it" is probably a legitimate defence, but the Score also probably predicts them getting beat up by the loved ones of whoever they hurt and being imprisoned. People like Mohs would make sure that they were allowed to carry on whatever they do until the Score said otherwise, then arrange for them to be arrested quicker than you can say "Bob's your uncle!"
OP is also missing a pretty big point in the game's logic, too. Even if someone did know they were destined to be a murderer or rapist, and did every possible thing to avoid it, even publicly refusing to follow the Score, they would end up committing such an atrocity anyway. That's why the detail about the Tower of Rem being a miner's city was added. The prophecy about the Light of the Sacred Flame leading his people to a miner's city and then causing his own death had to be fulfilled. The Score might not be fulfilled in ways you expect, but it is always fulfilled. What I thought was even creepier is imagining someone who would vow to never murder anyone, no matter the circumstances, damn the Score, and then imagining what kind of situation would have to happen for them to commit a murder. Then I realized - it would probably be something like the kind of situation that forces Luke to kill the guard on the Tartarus. Self-defense, nearly an accident, but somebody still died and it was Luke that did it.
Why do replicas have free will even though they're composed of the seventh fonon and thus completely part of Lorelei's fonon and in its power?This becomes clear when Lorelei tells Luke that Luke and Lorelei are one and the same being. According to the definition of a fonon sentience, Luke is one. Since Luke has the power of Lorelei and is equal to him, replicas aren't under Lorelei's jurisdiction, meaning he couldn't foresee their actions and include them in the Score.
The Japanese have a rather selective definition of what personal responsibility means, just like the Americans. That's why. Responsibility never attaches to the people who are the highest on the hierarchy, it's always the subordinates who should have done something. That's partially why the recent Fukushima disaster happened; the Japanese are not fond of whistleblowers (and even less fond of people who "make trouble"). To the Japanese, the idea that it was Luke's fault rather than the fault of the guy who manipulated him would seem to make sense. After all, Luke was the one who "pressed the button", so to speak. The fact that he didn't have enough information to make the right decision would simply not register to Japanese audiences. To them, "he pushed the button so it's his fault" is a simple enough explanation. It's how Americans think too, unfortunately; as long as you even bring up the word "responsibility", all thought seems to stop and the guy being accused of lacking it is automatically assumed to be at fault, no further investigation or level-headed inquiry necessary.
It's the same reason Asch has a grudge against Luke, transference. In both cases Luke isn't culpable in any way to either problem, but since both the party and Asch can't lay into the REAL cause Van, they're piling all of their anger and resentment onto Luke instead. In short, they need someone to blame and Luke is a convenient scapegoat. Luke was just a tool to Van, he's no more at fault for what happened to Akzeriuth than a gun is for the fact that someone fired it.
The Isle of Feres. Not so much the island itself, not within the realms of the universe, but everyone's reaction to and especially Jade's comment about it: "A floating island? That's physically impossible!" and yet... this is long after he learns the truth about the whole Outer Lands ordeal, where the entire world is floating. Admittedly they're two different concepts, but honestly, knowing that it's possible to make the entire world float would make it a lot more believable for a tiny island to be floating. It's just a little peculiar that everyone is so quick to be shocked that a single island is floating, even if the mechanisms used to make the world float no longer work. They're acting like they've never seen anything like it. It's just a little... weird.