Ape Shall Never Kill Ape: During the events on Leanbox where the trio agrees to help the Parliament with the Basilicom, IF specifically states the party will not get involved in missions attacking other humans.
Bittersweet Ending: After defeating the villain and destroying every monster in the world, the true ending has the four goddesses agree that if left alone, they'll only back to fighting one another. They ultimately decide to give up their power and immortality so a new goddess can be made to rule in their place. The epilogue even states that the world sees a new era of peace, while they grow old and eventually die.
Captain Obvious: Now and then Compa will exclaim "I don't like getting hurt!" upon damage. It's cute and funny the first time you hear it, but it may wear down on your nerves after awhile.
Character Blog: All three goddesses have one. They're mostly just Seinfeldian Conversation material, such as Black Heart going slightly cat-crazy and White Heart discussing how tangerines "kick ass."
Cool Ship: In the opening sequence, we see a jet plane while Neptune is being shown. Fans would assume that since this is an RPG, this is what people are gonna be using as a mode of transportation even though you don't travel on the world map. However, later on in the game, Neptune as Purple Heart gets a second Limit Break where SHE transforms into that jet and fires off a Wave Motion Gun. Sadly, no ramming attack even though the design really screams that the ship rams at opponents.
Neptune: Oops. Well, that was for ruining the moment.
The Dev Team Thinks of Everything: If you change Neptune's clothing and use her hammer skill in the field you can see that they took the time to change the color of her panties to match her stockings.
Disc One Nuke: Neptune's Neptune Break can be obtained at level 20, making you bulldoze the game for a long time. It's also your main damage dealer as well. Oh and you can spam it too.
Did You Just Punch Out Cthulhu?: You may have goddesses on your side, but several party members are just regular humans and only two of them have any serious combat experience. The game's backstory reveals that humans beating up an evil goddess has happened at least once before and the road to Celestia was sealed off to keep bad humans from attempting it.
When you are trying to rally a goddess under your banner, they will join you only if you beat them in a one-on-one. Green Heart, despite her passiveness during her arc, packs a bloody punch and can kill you in two shots.
Emoticon: Histoire seems to really like using this in her fairy mode.
Empty Levels: Anything past Lv. 99 can feel like this, as you get only one point per stat and no increases to HP or AP. The exception is Item Skill points, which increase by two and can help up the activation percentage rates.
Engrish: The initial names and descriptions for the trophies in the Japanese version had started out in English, but none of them seemed to have been proofread, so you get garbage like "deAtearmine" coming up. For reference, here's the trophy list for the Japanese version, and the list for the English version. Now, the English version's trophy list has superseded the Japanese one; anyone playing either version will see the English version's proper trophy list rather than the Japanese version's garbage one.
The Glomp: Neptune does this to Noire in one scene. She does it to Compa many times, too.
Gondor Calls for Aid: Neptune wants the other goddesses to help, but they don't want to. She has to beat the crap out of them again to make them help.
The Gods Must Be Lazy: The goddesses spend more time on their personal affairs and bonking heads than actually running their lands. Vert averts this later in the game by going out and actively fighting monsters.
Guide Dang It: It's an Idea Factory game, which means an incredibly obscure undocumented system must be used to reach the Golden Ending.
The game fails to mention that Neptune dying in battle has a hidden penalty and that if she dies too many times it can permanently lock you out of events — including the events to reach said ending!
Have You Seen My God?: Planeptune's Basilicom is understandably upset when Purple Heart doesn't show up when the goddesses start arriving. And in the Golden Ending, all four goddesses call it quits and leave Historie to create a new goddess to rule in their place.
Vert later calls IF Iffy (Ai-chan in Japan), which flusters IF to no end.
Thunder Tits for Green Heart, as coined by White Heart.
Ganache is called "Solicitor" by IF or "Mr." Solicitor by Compa.
Jerkass: Ganache, natch. He assigns the task of finding a rare ore to the party, and confines them in an abandoned building set to explode. Afterwards it turns out that was only a diversion, as stated by IF when Chian's factory is being sieged by Avenir robots.
Marathon Level: The "99 Knights" quest, which tasks you to take down 99 Turquoise Cadets. Assuming you get very lucky and get 3 Cadets every encounter, that's still 33 battles. And given that the battles only start after a fixed amount of walking around the map, walking around can easily take up a signifigant amount of time alone.
Mirror Match: Any of the CPUs versus their doppelgangers in the "Versus Fake * Heart" Quests.
Neptune: What's up? A favor? Ask me anything! Oh, but no touching. Got it? No touching!
Jade: Don't treat me like a pervert when I'm about to die.
Never Trust a Trailer: The game advertises that you get to play as the goddesses in the middle part (or at the very least, early-middle part) of the game. You only get to play with them in the final dungeon and possibly post-game.
Nobody Poops: Averted in one instance where Nep-Nep nearly misses out on Nisa's introduction by spending most of the preceding battle on the toilet.
Averted in another cutscene where Neppermint admits to being a little too excited about a visitor.
Face a foe who's a significant number of levels above you and Nep-Nep might start the fight by requesting a change of underwear.
Glimpsed when Neptune bends over while using her hammer skill.
The status of your characters covers it up until you press X to exit the battle, but Compa falls over after you win. The camera angle is situated in front of her so that you can see her undies for a brief second after the status leaves the screen. It's only for a fraction of a second.
Plot Tunnel: On the few occasions where Neptune leaves the party, you cannot leave that landmass until she returns. Justified in that she's the one who registered for permission to travel to begin with, and you'd need her for cutscenes in other landmasses anyway.
Rank Inflation: Most of the dungeons have timers on them. The faster you finish the dungeon via beating the boss, finding the secret treasure, or getting lucky with item drops from random encounters, the better your rank will be. This always often leads to a Bragging Rights Reward when you beat the record times of other players.
Skinship Grope: It's implied Neptune does this to Compa during one of the events when she invites her for some Bathtub Bonding, but nothing is shown except IF describing it.
Strongly Worded Letter: Played straight when Neptune and her friends send a series of threatening letters as a tactic to lure out Arfoire, Overlord Momus' messenger and separate her from a group of extremists she's leading. The plan actually works, but for a reason none of them expected - because Neptune misspelled Momus' name as "Overlord Moron".
Thanking The Player: In both endings, the main trio directly thanks you for getting them through the game.
Theme And Variations Soundtrack: Each landmass's theme is remixed for the landmass's dungeons as well as the battles within said dungeons. The title theme has also been remixed and used in various cutscenes.
Transformation Sequence: The four goddesses every time you have them transform in the middle of a battle. Fortunately, you can always skip it by pressing L2.