* AccidentalInnuendo: A construction worker in the Pyrite Hotel says "Apparently some rich fellow ordered the colosseum built. I'm amazingly stiff."
* BigLippedAlligatorMoment: In series canon the entire game and its sequel are one, as they have never been mentioned in any other games and both games have very noticeable quirks and are set in a WorldOfHam.
* BreatherBoss: After several tough rematches with the four Cipher Admins and before the battle with the head of Cipher, [[spoiler:Gonzap]] is actually not that tough at all. He even has some ArtificialStupidity, spamming Earthquake on the three of his Pokémon that have it, even though every time he does it, it knocks big chunks out of whoever else he has out at the time. Using Flygon makes it even funnier, since Levitate makes it immune to ground moves. His Shadow Skarmory can be a pain to catch, though. (Unless you swap-dupilicate the Master Ball, then it's a cinch.)
* CrowningMusicOfAwesome: Due to the increased space allowed by being on a console instead of a handheld, the soundtrack is much more grandiose than in any other Pokemon game.
** [[https://www.youtube.com/watch?v=X67YWv5C6qQ Miror B.'s Retro Groove]]. It's probably the most well-remembered theme from the game, and it's sure to [[EarWorm stay stuck in your head]] for quite a while after listening.
** Few songs have ever utilized a harmonica quite as effectively as the [[https://www.youtube.com/watch?v=j0HmO8MaCVo Shadow Pokemon Lab theme]].
** The [[https://www.youtube.com/watch?v=um0pkcPFCLs final boss theme]] is probably the most epic theme in the history of the series.
* FanPreferredCouple: [[AllGirlsWantBadBoys Wes and Rui]].
* FridgeBrilliance:
** At the beginning of the game, Es Cade promises to investigate Cipher for you. Yet throughout the game, he never once calls you to give you new information, and any time you visit him, what info he does have is stuff you've already known for a long while. At first it seems like he's incompetent, until [[spoiler: it is revealed that he's the BigBad]].
** Whenever you snag an Admin's Shadow Pokémon, in future battles, they will have a replacement for it. Gonzap will as well. When you fight Fein at the end, the man who is deliberately framing Wes for assault, his team (with the exception of Shadow Togetic) consists of the replacement Pokémon used by Gonzap and the Cipher Admins.
* EnsembleDarkhorse:
** Miror B. was popular enough that he was the only Cipher admin to reappear in the sequel.
** The other members of Cipher are this to a lesser extent, possibly due to the fact that they have their own unique Pokémon rather than the same Zubats that most other teams use.
** Wes is this among the main protagonists in the series. Unlike the others who are 11 year old kids, Wes is a 17 year-old ex-gangster with an overall cool design.
** Nascour for being a truly chilling villain.
* GameBreaker: The infinite ball glitch takes out any difficulty trying to catch Shadow Pokémon once you obtain the Master Ball.
* GoodBadBugs:
** You can use [[http://www.youtube.com/watch?v=PK4lMxx6YAc any Ball an infinite number of times by using it on your first mon's turn and switching your item list around in the second - and yes, this includes the Master Ball.]]
** If your AI opponent's last Pokémon faints to Burn or Poison while yours are under the effect of Perish Song, your Pokémon will receive triple the normal amount of experience.
** If you Snag a Pokémon on the same turn the AI tries to switch out, they will not send out a replacement for the Shadow Pokémon and the fight will continue as a 2v1 match.
* HilariousInHindsight: Ein's [[MagnificentBastard personality]], [[TheEvilGenius intellect]], [[TheManBehindTheMonsters creations]], and even hairstyle and dress sense are all very similar to [[Manga/{{Bleach}} Sosuke Aizen]].
%%* MemeticBadass: Wes.
* MoralEventHorizon: Dr. Ein crosses this just by ''inventing'' the Shadow Pokémon system (without a shred of remorse, and actually with a desire to ''improve'' it), and [[spoiler: Evice and Nascour]] just by leading the whole operation. Particularly [[spoiler:Evice, since he oversaw all these despicable actions while posing as the friendly mayor of Phenac City.]]
* MostAnnoyingSound: The alarm in the Shadow Pokémon Lab. It doesn't really do anything except annoy you, since the areas you've cleared out stay cleared. There's also no way to avoid it, as it's a scripted event that happens after defeating a required enemy. Worst of all is that it replaces the incredibly catchy background music.
* {{Narm}}:
** The tattoo Wes has, a horizontal white stripe over the bridge of his nose and cheeks, does not look intimidating at all.
** The reveal of the BigBad. [[spoiler:It's not the tall, cool-looking Nacour; it's the short, fat, ugly mayor of Phenac City. Who somehow floats]].
* RescuedFromTheScrappyHeap: Due to a lack of wild Pokémon and the ''extremely'' limited choices available to the player in this game (a total of 52 at the ''very'' end of the game) many Pokémon who are seldom used due to lack of usefulness in competitive play get the opportunity to shine here. One reviewer said it best in that this game forces you to use Pokémon you would usually never even think twice about just because of how few choices you get, especially early in the game.
* ScrappyMechanic:
** The move Shadow Rush inflicts [[CastFromHitPoints recoil damage]], which can deny you a Snag if the computer used it after you whittled a Shadow Pokémon down to low health.
** Hyper Mode forces you to forfeit a turn to dispel it, which can be frustrating if the Shadow Pokémon that contracted it is at low health and gets KO'd because of it.
* ThatOneBoss:
** Miror B. and his Ludicolo. The only weakness they have that you have access to is Flying, and only through a near-purified Noctowl/Swablu's Fly. They all have [[HealingFactor Rain Dish]] and know Rain Dance plus a group of restoring moves (Absorb, Leech Seed and Mega Drain) which make the fight take a long time even with Fly, since it's a two-turn attack.
** Dakim has 3 Pokémon with Earthquake and Protect, and they will alternate between them so one hits the entire field with Earthquake and the other doesn't take anything by Protecting. Earthquake also hits his Shadow Entei super effectively and it doesn't have Protect, so if you're not careful he'll knock it out and prevent you from catching it.
** Ein has three Confuse Ray users and two Toxic users to try and hax you out of turns and stall you out of HP with the passive Poison damage. His Lanturn and Huntail know Rain Dance to boost their Water attacks (and give Huntail a Speed boost since it has Swift Swim) and give Raikou and Lanturn [[AlwaysAccurateAttack 100% accurate Thunders]]. His team is also about 5 levels higher than the next strongest trainer you fight, so he may also overpower you by level advantage if you haven't been grinding.
** [[spoiler:Evice]], especially if you allow Slowking and Slaking out together. Slowking WILL use Skill Swap and Slaking will use its high base stats and freedom from Truant to destroy your team. His others are no slouch either, since they all know moves that will boost their Attack. Of note are his Salamence with Dragon Dance and his Scizor with Baton Pass so it can pass Swords Dance boosts to a teammate.
* ThatOneLevel:
** The abandoned mine hideout of Miror B. It's a maze of tunnels and bridges and caverns and they all look alike. The random trainers scattered throughout will have you jumping for joy when you stumble onto the heal machine before the boss battle. Although you get a cut scene skip to Duking's house after battling Miror B, you have to find your way in and out on your own when you go after [[BonusBoss Mirakle B.]] And if you thought you could use an Escape Rope like in the handheld games... you can't in this game.
** The Shadow Pokémon Lab has a very linear layout but has two major annoyances. First there is only one PC where you can save which is located at the beginning and no heal machine at all; then there is the other problem of cipher peons dropping in (literally) and ambushing you when your Pokémon are weak.
** Realgam Tower has a lot of tough battles to get through, several of them with Cipher admins, and the level spike of Nascour and [[spoiler:Evice]] means you have to grind to stand any chance of beating them. Nascour is in the 50s, and [[spoiler:Evice]] at 60-61. Plus, you can't save after each battle in the final part, meaning you have to deliberately lose to one of the normal trainers and then save to secure snagged Shadow Pokémon (fortunately you're healed after each battle). However, Nascour and [[spoiler:Evice]] are both much higher than anyone else you've faced, and you likely won't be strong enough the first time you fight them.
* TheyWastedAPerfectlyGoodCharacter: The Plusle that Duking gives you is a JokeCharacter in-game. However, if the developers had made Minun obtainable, as DummiedOut text from Nett suggests they had at one point planned to, it could have been a rather good option. The abilities of Plusle and Minun, Plus and Minus respectively, raise the Special Attack of both Pokémon if they are allied with each other. Considering this game is all Double Battles, it's rather frustrating that they didn't end up including Minun.
* UncannyValley: The way Rui's eye bulge to the sides makes her face quite unsettling.