These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Awesome Music: There's a lot of really good music. Arguably, it's even better than Breath of Fire 3.
Complete Monster: Yuna comes off as little more than a self-righteous, smarmy little git until you complete the dungeon of his lab and you see that he's taken Nina's sister and made her into some sort of genetically modified horror. Him telling all about the 'wonderful gift' he's given her, looking for some kind of praise, makes it clear how irredeemably evil the guy actually is. Yuna also built a weapon of warfare that launches Hex, a toxic gas, physically. It's actually the souls of people tortured at the hands of Yuna and the more anguish they have, the better the effect. You can see this in a side event and its effects are presented in the village of Chamba in the beginning of the game. The way the player experiences its horror just drives the point home. At one point in the game, we are introduced to Mami, a genuinely likable love interest for Fou-lu. Just as it seems she's going to reform him, she's taken away and tortured to the point of insanity so she can be used to fuel an attack against the poor guy. When he discovers this, he decides that Humans Are the Real Monsters and becomes intent on destroying them. To add insult upon injury, Yuna slithers from the chains of karma, since a player doesn't get to splatter the guy's innards all over the place. In the ending, he even smugly claims he will do it all over again. According to the creative team, a player was supposed to get around to tearing him a new one, but the suits decided rushing the game out was more important than actually finishing it.
Using the Kaiser is a lot more tolerable this time, since you can EASILY stock up on Wisdom Seeds by shop in the Fairy Village. And find all the dragon summons? WIN.
If you fought enough battles and know how to set up your characters, the Render is this.
Love to Hate: Yuna. Despite quite possibly being one of the most disgustingly evil villains in the franchise whose actions cannot possibly be defended, he's quite popular with the fanbase. Admittedly, the majority of that group wants to see him die in a fire for all he's done, but he's still widely regarded as one of the better antagonists.
Moral Event Horizon: Yuna crossed this before and during the storyline on several occasions. Elina's state when she's found was his doing and he gleefully described what he did. In the ending, he implies that he's going to continue his work.
Yohm crosses this when he sends Mami to be used for the Carronade.
Nausea Fuel: Fairy Drops. You start out thinking it's a stone or a precious metal. Turns out it's actually Solid Gold Poop, complete with a scene where the fairy is obviouslydropping a deuce behind a bush. Eww. Made even worse with Nina commenting on how "pretty" it is, and Scias being the sole member of the party even remotely disturbed that they're admiring fairy turds.
Nightmare Fuel: Take your pick: nuclear-weapon-like cannons that require human sacrifice; Nina's sister being turn into an immobile, immortal creature; or the fact that Cray was the one who had to mercy-kill her.
The Scrappy: Mami's landlord, who does nothing but tell Fou-Lu to leave and badmouths him. She ends up responsible for Yohm showing up and Mami being used for the Carronade to attempt to kill Fou-Lu.
That One Level: Kyria and all of the time wasting traps, especially in the woods where you need to find the mayor and track the monster.
Synesta, where the party must take on the exceedingly difficult task of chasing down an incredibly fast orphan.
You desire to beat I and II at the Emperor's Tomb? No dice. However, there's actually a way of fighting them that forces them to use the attacks you want. Good luck figuring it out on your own though. The whole thing isn't helped by the annoyingly long dungeon (with puzzles) and another boss that will have occurred between your last save point and I and II.
Both Won-Qu and A-tur are difficult. Won-Qu is difficult due to his ability to deal more damage then you can heal, and unless you have armour from the last town you visited that made water deal less damage (Since Ryu takes extra damage from water.), you're going to be in even more of a world of hurt.
A-tur's real difficulty lies in the fact that he's a stronger version of Won-Qu and he has Sanctuary, which nullifies any buffs your party may have.