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.
The fans are not pleased for Yuu replaced by Lenka in the anime adaptation, the fact why he's disliked because he is generic, Anime Hair, hotblooded, and serious. Meanwhile, Yuu is caring, polite, but by no means, useless, quite the opposite in fact, as shown in light novel/manga adaptations.
While the other fans disliked Yuu because in the actual game, he is a generic lead and lacks both backstory and personality. This applies especially to people who never read the light novel/mangas. Meanwhile, Lenka have some unique/special traits and has a backstory.
Only time will tell which one is a better protagonist.
Evil Is Sexy: The DLC Aragami may count for this, the human parts of her are quite sexy. Too bad the rest of her body kind of ruins it.
The same can be said of any of the other Aragami that take on some semblance of a humanoid female. Arda Nova, for example, would look completely human (and extremely sexy) were it not for the unusual skin coloration (magenta).
Game Breaker: God Eater 2 and Rage Burst are notorious for this.
The Impulse Edge is Simple Yet Awesome, being able to confront a wide variety of Aragami (from being able to bash open a Borg Camlann's shield, to being able to ruin a Quadriga's day by hitting the front treads) with relatively little difficulty.
The infamous meteor bullet will let you deal more than 100,000 damage against the Aragami. An update patch reduce its power to half, but it's still broken.
Goddamn Bats: In early missions, the goddamn Chi-You and its goddamn damage-resistant legs and its goddamn fast-startup melee attacks that also let it move across the map quickly. Nowhere near Demonic Spider status since it remains killable and doesn't hit too hard, but still highly irritating.
Zygotes become a textbook example of this in mid-game level quests, taking precious seconds to kill even with a level-appropriate upgraded weapon, hitting you with various debuffs, and/or just distracting you from focussing on the boss.
Harsher in Hindsight: A DLC mission for God Eater 2 (included in the Updated Re-release) titled "A Promise to be Fulfilled" features Yuno, Satsuki and BLOOD going on a picnic (Or what's left of BLOOD anyway). It reveals that the picnic mentioned earlier in the story, which we never got to see, was interrupted because BLOOD was ordered to deploy. All of them then promised to continue the picnic some other time, which makes Romeo's death and Julius's Heroic Sacrifice all the more tragic.
No Export for You: Not for the game itself, but for later versions of its DLC. There is demand for it amongst its players, but D3 Publisher bluntly stated on their Facebook page that they would not bring them over to the English version due to localization issues (i.e. the third-party promotional/collaboration items).
The Borg Camlann line's tailspin and Arda Nova's combination attacks can be a pretty rude awakening if you can't see them coming.
That One Quest: "Cowboy" will be this for some if they did not read the quest objectives (or read and ignored it, not taking it seriously). Here's how the quest goes, there are four mooks and one boss. The quest says only to kill the mooks. Guess what a lot of people tried to do... And that doesn't even take into account the times where the boss is dead-set on ruining your day while you just want to finish the mission properly.
The temple where you have to kill four kongous, all of different elemental types.
Your first attempt at the Vajra, Ouroboros, Prithvi Mata, Arda Nova, or any of the major bosses.
Thor's Banquet. Your objective? Kill four Vajras. Alone. And they usually all spot you the very moment you leave the safe zone. Good luck.