Before the Demise, which is actually the final boss theme. It's most unlike final boss themes, which are often trying to pump you up.
The DS version's opening theme, Follow the Nightingale. Also doubles as the music for Mathias's final form in Innocence R.
Demonic Spiders: After the events at the Sky Castle, Luca is dumped into the desert, separated from the rest of the party, and has to make his way to a nearby town. Some of the enemies can petrify on attacks, and if your entire party is petrified, game over. Your entire one character party. And if you didn't save before attempting to cross the desert, you get to sit through a long cutscene again, too. Luckily, the town is very close by, so it's quite possible to bypass battles.
Ensemble Darkhorse: Spada, at least in the Japanese fandom. He is the only character from Innocence to appear in the top 30 of Namco's popularity polls, not to mention appearing twice, in the 4th and 5th polls.
Ho Yay: Due to the nature of Relationship Values, players can pair Luca with whoever they want (at least, in the original version). There are some notable ones story-wise, though, especially in R.
In the original, when Luca recovers after he was stabbed by Hasta, Spada hugs him◊ twice (and attempted the third). In R? It goes way back to early in the story not long after they meet, where upon finding out that Luca is the reincarnation of Asura, Spada immediately hugs him while telling him that he (as Durandal) missed Luca/Asura...before it is humorously cut short by Iria. Luca's reaction does not help matters. In R, they are upgraded to Bash Brothers, with some of their victory poses have them cross their swords in the air together.
Kongwai/Luca. In the Relationship Values screen, Kongwai notes Luca to be "interesting", among other things. He is also one of a few who actually treats Luca well.
For some Les Yay in R, Hermana's obsession with Ange's assets now manages to give Spada's a run for his money.
The past life side has Himmel and Orifiel, who mean so much for each other that Albert/Himmel intended to sacrifice Ange/Orifiel to activate the Manifest.
Older Than They Think: Much of the game's premise is eerily similar to the backstory of White Wolf's Exalted RPG, down to the past-life superpowers and conspiracy about the downfall of the main character's previous incarnation.
Player Punch: In the Tower of Dawn, Luca and Co. are confronted by Oswald piloting the new-and-improved Gigantess Omega and reveals, too much to Ricardo's horror, that is powered by Gardel/Thanatos' corpse. Ricardo swears that Oswald will pay for desecrating the remains of his brother. The party, too, is more than ready to rip Pigwald a new one.
That One Boss: Despite the different balance and progression issues between the DS version and R, the bosses that were a pain in the former continue to be a pain in the latter.
Hasta. As if his pre-battle cutscene ramblings haven't disoriented you (and the party) enough. Hasta has nasty offensive and defensive power to begin with, and this is made worse by his Weapon of Choice, meaning he has wide range for his attacks. The DS version was even more merciless with him, since he brought monster companions and appeared at the end of extremely frustrating dungeons.
Chien is much more dangerous; he's fought two times, and both times together with his two dogs. Both of which has stats like a standard boss. So yeah, he's a triple-boss. Seriously, good luck.
Oswald. You'd think a fat, incompetent opportunist would be a pushover in a boss fight. Nope! He comes in on the party with the experimental Gigantess Omega. Made to take on Mathias. Fighting the battle is hell itself. His kicks, dashes and shots deal insane damage to the party, but to make things worse, his tornado is pretty much guaranteed to KO anyone near him who weren't quick enough to guard or move out of the way. Oh, but that's not even his trump card: he has an energy surge attack that knocks down and away anyone near him (i.e:the melee fighters, who are the #1 powerhouses) while dealing nigh-OHKO damage at the same time. And he uses it without any warning. Did we mention that he's constantly on the move, rarely touches the ground and never stays in one spot for more than a few seconds, while also boasting ridiculous physical defense that render your frontliners little more than useless?
The battle with Ange and Albert. One's way stronger than a boss has any right to be, and the other interrupts everything you do with gun attacks. Every time you wanna use an item or start casting a spell or do anything, he shoots you. And his gun causes two of the Standard Status Effects. And they can heal. A lot. Pure irritation.
The Scrappy: Coda. It's not that he does something to be hated - it's that he doesn't do anything at all for the whole game. He has no backstory and no plot purpose. He's just there for the sake of being the game's mascot and tutorial. And rag on about food. The game actually acknowledges this numerous times, so this is most likely intentional.
Viewer Gender Confusion: Himmel. His hair is caught in a long, flowing, braid, his outfit is very androgynous and his face is probably more feminine than anyone else's. His voice doesn't help.
When you think about it, Thanatos actually counts; cast down from Devaloka for falling in love with a human girl, his peerless love for her spread to the whole Naraka itself, pushing him to protect it at all costs. To think he'd meet his end at the hands of one of his descendants... <Sniff>.
Chien too, definitely. He was shunned by the society thanks to the fact that his dogs, Cer and Ber, are actually his biological brothers (being the reincarnations of Cerberus), prompting him to join Arca cult under the hope he could finally be accepted. Then Mathias reveals her nature as Omnicidal Maniac. The kid really needs one of Ange's hugs.
"AKAYum Yum", the very final recipe, which can only be obtained after getting every other recipe in the game, and a key item. The effect? 90% EXP bonus for 9 turns. Now, get grinding!
However, the one that ultimately takes the throne here is the recipe that comes just before it: "Manhan Quanxi"note The Manchu Han Imperial Feast. It requires 9 types of ingredients in varying portions, which makes 18 portions per dish, and lasts for only one turn. What does it do? 40% DEF bonus, and 80% Physical damage reduction. It's practically made for boss fights, and indeed, makes them ridiculous it does.
The final ability unlocked by Versus Style; you know, the ability that grants no stat bonuses and only unlocks self-crippling abilities? "Risk & Reward": -90% HP for +90% EXP bonus. Even discounting the cumulative EXP you can milk together with "AKA Yum Yum", the ability alone is pretty much gamebreaking if you can defend/evade well.
Woolseyism: The fan-translation takes this path for a good fraction of the game, which is noticeable if you listen and cross-check the voice-acting and translated scripts. They don't translate word-for-word, and instead focused on fluency. The very first example is replacing "Tenjo" and "Chijo" with "Devaloka" and "Naraka", which is Sanskrit for "Realm of the Devas"/"Heaven" and "Hell" respectively. It makes sense in context of later revelations, as the game draws a fair amount from Buddhism and Hinduism. And you know, if literalism is your thing, you actually have the option of turning off the Woolseyisms...for terminology, anyway.