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.
Family-Unfriendly Aesop: The Emperor who attacked and mutilated a deity to save thousands of his people from dying in a drought is vilified for it, while the deity who caused said drought is treated sympathetically. And that's not even the tip of the iceberg...
Although given that after ending the drought, the Emperor goes off the deep end, proclaiming himself a god, then has golem factories kill people for the sake of his golem army, he's definitely still a villain. And then there's the whole "no one can enter the afterlife, therefore nobody new can be born so the world will be infested by ghosts" thing. And then there's the fact that in "stopping" the draught, he merely shifted the problem onto someone else.
Mirabelle, a gun in a setting with swords and fists, though its somewhat balanced by the large amount of focus and the time needed to load after each shot.
The time needed to load after each shot is significant even when fully upgraded, it can misfire, and it's arguably not powerful enough for its rate of fire.
It is the most rigged thing ever in the arena though due to the fact that you are usually fighting one on one and it deals enough knockback to throw the opponent far enough away that you can reload another shot
The Jade Golem transformation is completely unbalanced and will break through pretty much anything in seconds while exposing the player to almost no damage, even when fighting the game's final boss enemies. While there is a Chi drain active while using it, battle tends to end so quickly with it active that you lose little Chi (and one of your party members can simply meditate and constantly restore your Chi anyway.)
Oddly, the Jade Golem is weakest to, well, groups of Mooks. Jade Golem's strength comes from being invulnerable to all status effects and most advanced attacks... which Mooks usually don't have. Groups of Mooks can simply surround you and whale on you, chipping away at your health while you slowly kill them one by one.
Before the Jade Golem transformation is unlocked, there is also the Storm Dragon style which has a near ten-second stun effect, during which the play is free to attack away with impunity. Combined with its resonance combo producing an endless supply of Focus orbs, the player can easily activate and remain in Focus Mode for the entire duration of combat so long as the combos are activated. This was the only style significantly changed for the "Jade Empire In Style" mod. This effect does not work on ghosts, however - and many of the harder enemies cannot have Resonance Combos used against them. The Jade Golem transformation, on the other hand, works on everything.
Earlier still, Toad style is pretty unbeatable too.
Paralysing Palm. Hit your enemy a few times, go into focus mode, switch to a damaging style, go to town. Notably, it's more-or-less a cut-down version of Storm Dragon.
Hell, at the default difficulty even the sword you get a few minutes in will make you an unstoppable whirlwind through most of the game as long as you upgrade the style and buy the upgrade later. The dual-swords style makes everything but spirit fights from that point on a total joke even at the hard setting. Dual-axes are even worse, if only because it doesn't cost Focus points to use when fully upgraded; however, if you can kill the guy who carries the Tang's Vengeance axes, you probably don't need them anyway.
The forward flip evasive move allows the player to easily avoid almost every attack the game can throw at you, hitstuns all but the larger enemies in the game if you land on them, and puts the player in the perfect postion to hit enemies a couple of times before they can turn around even if they haven't been hitstunned. A typical battle with a player that has realized this will probably be something like: Flip! Strike! Flip! Strike! Flip! Strike! and so on and so on. it makes it incredibly easy to curbstomp countless battles against multiple foes in succession without ever taking a hit.
The simple act of switching styles in the middle of a standard combo can be repeated for eternity, stunlocking many enemies into oblivion. Combine that with a slowing status effect and most enemies simply cease to be problems on their own.
Goddamn Bats: Lost Spirits attack in groups (that tend to be spread out), have ranged attacks that drain both your HP and Chi, and give ridiculously paltry EXP. They turn into Demonic Spiders when they're supporting an actual dangerous boss. Also, they respawn.
Ghost Lords are equally annoying - their attacks are less powerful, but they have ridiculous amounts of health.
Sun Li, however, actually is. He and Rommel share more in common than "just" tactical genius.
Moral Event Horizon: Sun Li crosses it for the player when he kills them and reveals that he was using them as a pawn the entire time, and then crosses it for Dawn Star, his own daughter, during the final battle when he coldly brushes off her attempts to reason with him and smugly declare that she was "just another tool".
Emperor Sun Hai crosses it when it is revealed that he was knowingly responsible for everything the Lotus Assassins did.
As a child, Captain Sen let a young boy die to avoid getting in trouble.
In the eyes of Dawn Star (unless Closed Fist romanced), Silk Fox (unless Closed Fist romanced), Sky (unless Closed Fist romanced), and Henpecked Hou (always), you cross the Moral Event Horizon if you bind the Water Dragon's power to yourself instead of killing her and releasing her from the machine.
Spiritual Licensee: Jade Empire is not a straight rip-off of Bridge of Birds, but it is certainly heavily inspired by its concept and takes several important character names (Master Li, Henpecked Hou) straight from the novel, although the characters themselves are different.
Additionally, "Lu the Prodigy" seems much like Lu Yu, a.k.a. Number Ten Ox, and they share a plot point: a flooded city hiding a secret artifact.
That One Boss: When playing with Jade Master difficulty, the Dirge clones become this. With normal difficulty, you can use the Jade Golem transformation style and/or focus mode to beat them easily. However, with Jade Master difficulty all the enemies can take much more damage than in the normal mode, which means your magic and focus bars have probably run out before you've defeated even one of the three clones. The only way to defeat them without insane amounts of practice and very good reflexes is to exploit the weaknesses of the game's AI, and even then it's hardly easy. Compared to the clones, the final boss of the game is much easier to beat, even with Jade Master difficulty.
That One Level: Rather late in the game you are killed, must navigate the afterlife and the defiled temple of the Water Dragon, and face one of the hardest battle in the game against three very tough copies of yourself, in order to be resurrected.
Vaporware: BioWare stated in the past that a sequel was planned and apparently at one point was actually in development, though it vanished in the wake of the EA buyout and hasn't been heard from since. Concepts from it have found their way into Mass Effect and Dragon Age, however.