Breather Boss: Belphegor. Most of the other Archdemons have a repertoire of nasty tricks that can be difficult to manage. His gimmick, however, is that he just changes his elemental affinity whenever you hit him with an elemental spell, and he only uses one at a time. So if you stick to non-elemental attacks he'll never switch off of Fire, and by adding an Elementalist to some anti-flame equipment you can reduce his maximum damage output to 1. Given that he guards Lux (a spell that makes all the other boss fights much easier), this may be intentional.
Faux Symbolism: While it's not directly mentioned, each town represents one of the Seven Deadly Sins, and in the second half of the game is haunted by a demon also representing the sin.
The moment you hit Urbeth (at least after the Liberte arc), the merchant town, which sells very powerful magic very early in the game. It's expensive, but the same town hosts a shopkeeping minigame which can be easily exploited for massive cash, and even has several very short and easy sidequests to provide seed money. As if that weren't enough, there's a crown obtained in the same town that's powered by money. It's barely even an exploit. If you've been hanging onto all the curative items and low-powered gear you'll have acquired by this point, you can make a tidy profit just selling off your accumulated Vendor Trash. Once you start buying things in order to sell them, though, you're essentially only limited by your patience.
A simpler example is Magic Might, the ability learned by fully upgrading the Black Mage crown. Pretty much instant victory in any battle that isn't a boss fight, and makes boss fights MUCH shorter.
The Elementalist's "Mysterio" spell gives the whole party resistance to all elemental attacks. If any characters already had resistance to any elements before it from equipment, they will be healed by attacks of those elements. Needless to say, Darkness-resistant armor and Mysterio are definitely your friends during the endgame.
Iron Woobie: Yunita, a Failure Knight who tries to rescue Aire on her own then gets yanked by Brandt, who ditches her in a misguided attempt to look like a strong, independent hero after the Sand Devil is killed. Jusqua later finds her in Urbeth dressed in rags, wallowing in self-pity and initially turning down Jusqua's attempts to make her join him and lift a curse on Aire (or so he thinks). And after the pair save Urbeth from a monster outbreak, he ditches her too. Worse still, she's not gaining EXP during all this, meaning that when she does finally rejoin, she's vastly behind the rest of the party. The kicker would be when Aire and Brandt have a conversation where she asks him if he dumped her for getting in the way and then chides him because he should know she's useless on her own. Man, no respect!
Scrappy Mechanic: The autotargeting. Basically, you can't select an attack target, the game does it for you. For physical attacks, it selects the frontmost leftmost target and for magic attacks, it selects the backmost rightmost target. This makes strategic plays incredibly difficult since you can't select the optimal target for your attacks or spells and leads to many many frustrating incidences where one enemy needs taking care of significantly more than the others, but you are unable to specifically direct your attacks at it without wasting AP to use an AOE attack that might not even be very effective or first taking out the adjacent enemies for the game to register it as the appropriate target.
Tear Jerker: Traveling to Urbeth in the past and learning that Thauzand was a priest who lost his faith because he couldn't afford the medicine to save his daughter's life. Thankfully you change history so she lives.
That One Attack: Asmodeus' "Sidewinder" is easily one of, if not the, most infuriatingly powerful attacks in the game. See That One Boss below.
Beelzebub's "Fall of Angels", if you don't stop it in time, can be absolutely devastating to your party if it doesn't kill everyone first. It's a massively damaging attack that hits everyone and is very difficult to recover from.
In the same vein as Beelzebub, Leviathans "Tidal Wave" can absolutely devastate your party if you don't stop it in time. Unlike Beelzebub, you can pretty much nullify all damage by equipping ice-resistant armour.
Lucifers "Judegemnt Bolt" has the nasty effect of reducing your party's AP to zero. Even if you're prepared for it, it is still gonna throw you off.
Trollud certainly has tripped up some players who weren't expecting a boss to buff its stats so soon
Arbaroc is pretty difficult too, without the right equipment and crowns. If you don't start taking pre-preparations for battle seriously, you're going to find this boss hell.
The vast majority of bosses in the second half will kick your ass to hell and back, even if you've figured out the trick to beat them. To wit
Asmodeus: Not only does he take ages to whittle down (thanks to all his snake heads), but he can demoralize your party to severely cut down their stats and cast several powerful magic attacks that can hit everyone. And that's not even mentioning his That One Attack: Sidewinder. Not only does it hit everyone for massive damage, it also inflicts every status ailment at once. Simultaneously. If you don't come prepared (hell, even if you do come prepared) you are gonna have a real rough time
Belphegor can be this if you get too used to using specific elemental attacks. If you're not carrying any non-elemental attacks/spells, the fight can become a massive slog trying to figure out his current weakness. And all the while, he's got a bunch of annoying cubes throwing elemental magic at you. Of course, if you managed to get Magic Might...
Lucifer: A meaty challenge of its own, but the one thing that Lucifer can do that makes him so frustrating compared to other bosses (except perhaps Asmodeus) is his special moves that drains all of your AP! Coming back from a blow like this is phenomally difficult if you aren't prepared and can seriously disrupt your strategies.
Mind you, in regards to the bosses of the second half they become a lot easier when you fight them again in the Star Chamber (except Beelzebub for some reason) once you've obtained the weapons of light and levelled up your abilities and equipment. Although given you lose all your crowns when you first enter the star chamber, what order you fight them in determines just how much easier (or harder) they will have become.
There are actually only two dead ends. The problem with this is the fact that everything looks the same, so even if you know exactly what you did wrong, backtracking is frustrating enough to want to throw your DS at the wall. And the worst part? The Start Chamber is the dungeon prior to reaching the final boss, who lurks in — of course — the last room. The only save point is at the entrance to the Star Chamber. Oh, so you lost the final boss fight? Congratulations, you get to traverse the hell dungeon again! Forget saving the world; not having to slog through that friggin' dungeon again is more than enough motivation to throw your all into that final fight.
To truly highlight just how ridiculously confusing the area is: the official strategy guide comes with a very clear map of the Star Chamber to help you on your way, but take heart! You will be not be referring to it for guidance at every corner. No. You will be referring to it for every step you take, because thanks to the level design, you might as well be wandering through Rock Tunnel without Flash.
The sequences where one character is running around solo. They're not otherwise harder than any other part of the game, but the fact that you cannot flee without using the Wayfarer job and the inability to save on the world map makes it more nervewracking than it should be. Aire's stats are actually reduced during her jaunt because of her animal form. (Making it worse is that, except for Yunita's, it's all the result of their own foolishness.)
Rekoteh. She's parted from her beloved brother Rolan for centuries when he's sent off to be a hero for the whole world. When the party meets her, all she wants to do is visit Spelvia to see if he's all right, and when she gets there, it's to find that he's been consumed by hatred and darkness. When the party goes into the past, it's to find that Invidia's endless winter is not natural and has turned everyone but Rekoteh cold and bitter. Her father in particular treats her terribly, saying she's inferior to her brother and casting her out of the house.
Woolseyism: The localization changes a number of the crown names from their intended meaning, which may be an attempt to parallel how some of the Japanese name jobs are different from usual (like the Black Mage being named Kuromahōtsukai instead of the usual Kuromadōshi). To wit:
"Yakushi" (Pharmacist) became "Salve-Maker".
"Budōka" (Martial Artist) became "Fighter", which thoroughly confused fans of Final Fantasy I and Dungeons & Dragons who might expect something closer to a swordsman.