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.
YMMV: Fall from Heaven
Complete Monster: Auric Ulvin, who sacrificed the peaceful Cassiel in a sufficient gory way to make the Doviello warriors have some (few) remorses, gave the mercenary-king Tasunke as lunch for his dragon, and performed a ritual consuming the souls of the Illians. And why? Only for the sake of making Erebus return to a new Age of Ice and reign on it as god.
Designated Hero: The game runs on Black and White Morality, but many of the "Good" factions are Ax-Crazy and so devoted to the destruction of evil that they don't care who they kill in the process (or in the case of the Mercurians, actively encourage the death of good people so they can be reborn as Angels to defend the world).
Which is rather possibly intentional, even the leaders branded as good are incredibly anti-heroic and such, emphazising the Crapsack World Erebus actually is.
Epileptic Trees: Many, many examples regarding lore that hasn't been fully explored.
Game Breaker: Without a doubt, Chalid Astrakein is one of these. The Religious Hero of the Empryrean, he possesses a spell, Piller of Fire, that turns enemy deathstacks into an absolute joke. Basically, every time he casts it (and he can cast it every turn) the largest stack within two tiles of him gets absolutely devastated. It doesn't matter how many units are in there, they will all take tremendous damage, leaving them with only 20% of their health, and thus, 20% of their attack power. It can't outright kill them, but since losing health weakens their fighting power, the stack is easy pickings for your army.
That One Boss: Any enemy civ's Hero Unit would count, but the most notable ones among the barbarians are Orthus, a warlord who appears early in the game to terrorize and eliminate any unprepared players who happen to be nearby, and Acheron, a really nasty dragon who is supposed to be optional but may spawn right outside your borders. The most irritatingHero Unit is Loki, who can't be killed unless he is surrounded or in a city. This wouldn't be so bad except for the facts that he can enter enemy borders at will and flip cities without culture, such as all new cities unless you have a certain trait.
Unfortunate Implications: Likely because of the exotic feel of some of the languages used in the original game, many of them have been recycled for this mod. This creates an unfortunate situation where some of the more morally ambiguous cultures are represented by real world languages. The Balseraphs speak French, though this may be a Shout-Out to Cirque du Soleil.
The cinematic for founding the Ashen Veil, the aforementioned completely irredeemable Religion of Evil? A statue of the Buddha. Appropriately redecorated, of course (all but two of the religion cinematics are just retextured versions of the Civ4 ones), but still, Symbolism Backlash much?