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.
Accidental Innuendo: A construction worker in the Pyrite Hotel says "Apparently some rich fellow ordered the colosseum built. I'm amazingly stiff."
Big Lipped Alligator Moment: In series canon the entire game and its sequel are one, as they have never been mentioned outside of the descriptions of Pokémon traded from them, and both games have very noticeable quirks and are set in a World of Ham.
Breather Boss: After several tough rematches with the four Cipher Admins and before the battle with the head of Cipher, Gonzap is actually not that tough at all. He even has some Artificial Stupidity, 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.)
Fridge Brilliance: 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 it is revealed that he's the Big Bad.
You have a chance of finding Shiny Pokémon even though they aren't supposed to appear. There is no guarantee they'll stay shiny after purification and trading to another game.
Hell Is That Noise: Right before the battle with Nascour, a rather intimidating villain overture is playing as he approaches you. This by itself is rather eerie, but it's even worse due to the fact that the audience of Realgam Tower's colosseum is chanting what sounds a lot like "KILL! KILL! KILL!" The feeling of having the audience actively rooting against you while you're going toe to toe with the false head of Cipher really helps with setting up an ominous atmosphere.
Moral Event Horizon: 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 Evice and Nascour just by leading the whole operation. Particularly Evice since he oversaw all these despicable actions while posing as the friendly mayor of Phenac City.
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 Big Bad. It's not the tall, cool-looking Nacour; it's the short, fat, ugly mayor of Phenac City. Who somehow floats.
No Export for You: The game has e-Reader support, but none of the cards were released outside Japan. Defeating the trainers on those cards unlocked three more Shadow Pokémon (Togepi (though you can get Shadow Togepi in the sequel's main game), Mareep, and Scizor). Plus the bonus disc's Celebi. Those outside Japan only got Jirachi on the bonus disk.
Play the Game, Skip the Story: Fans and former fans demanded a more plot-driven Pokémon game or for a Darker and Edgier entry to the series. They get Colosseum and...the responses are either "WTF where are the wilds?" "Why is this not like Pokémon Red or Blue?", "Shadow Pokémon? WTF are they babbling on about I wanna EV train!", "Double Battles? I HATE Double Battles!", while the Darker and Edgier stuff was mostly completely ignored by the "Pokémon is kiddy" age-ghetto types.
Although some people actually did pay attention. This is like the Ensemble Darkhorse of games in the franchise, after all.
Rescued from the Scrappy Heap: 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.
Scrappy Mechanic: Shadow Rush in Colosseum inflicted recoil damage, which the computer tended to use to deny a Snag by forcing a self KO (Which is really annoying with Colosseum's use of Save Points and leads to much back tracking). This is fixed in XD. Now there are more Shadow moves than Shadow Rush and only Shadow Half (reduces the HP of all Pokémon on the field by half) and Shadow End (deal great damage but reduces the user's HP by half) have recoil (both appear only on end-game snag targets),aside from the usual recoil moves like Take Down, Double Edge,ect, but they have the same lethality as False Swipe, which benefits the player.
Hyper Mode in all its lose a turn glory - especially if said Pokémon is low on health and likely to get KO'd before being able to take the opponent down first.
Can be seen as a blessing if you're interested in purifying all Pokémon quickly; the Pokémon at a cost of a lost turn by calling it will also gain happiness points, reducing the amount of time needed to purify it.
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 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 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.
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.
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 Mirakle B. And if you thought you could use an Escape Rope like in the handheld games... you can't in this game.
Realgam Tower has a lot of tough battles to get through, several of them with Cipher admins, and the level spike of Nascour and Evice means you have to grind to stand any chance of beating them. Nascour is in the 50s, and 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 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.
Uncanny Valley: The way Rui's eye bulge to the sides makes her face quite unsettling.