* ContestedSequel: To ''VideoGame/PokemonColosseum''. While it cleaned up a lot of the criticism that game got, certain things, such as the less involved plot, the LighterAndSofter take on Orre, and in general recycling a lot of plot elements from Colosseum made many feel like this game was a step backwards. The only thing people never seem to criticize is [[EnsembleDarkhorse Shadow Lugia]].
* CrowningMomentOfHeartwarming:
** Shadow Togepi's backstory: you have the option to trade it back to Hordel, with him giving you an Elekid with a unique moveset (if you give him the Shadow Togepi in particular). But you can feel his joy when you give the Togepi/Togetic to him. You can tell he genuinely cared for that little guy and wanted him to be purified as a personal favor, because he grew attached to it.
** If you beat [[spoiler: Greevil]] again after purifying all Shadow Pokemon, you'll see a brief cutscene of the hero putting his Snag Machine away, as it's not needed anymore. Gives a nice feeling of closure.
* EnsembleDarkhorse: [[EvilIsCool Shadow Lugia]] for being utterly badass and Miror B. (again) for being hilarious, LaughablyEvil, stylish, and having awesome music, are the most remembered characters in the game. Even to this day there are several fans demanding that they both make another appearance in the series.
* FashionVictimVillain: Snattle's outfit consists of a BadassLongcoat combined with what appears to be a white jumpsuit underneath, with what appears to be a massive mood ring around his neck. His purple lipstick and bizarre hat (or possibly hair) don't do him any favors, either.
* FauxSymbolism: All the protagonist's default names in the English version (Michael, David and Adam) have Biblical connotations.
* FoeYay: After being defeated at Orre Colosseum, Lovrina takes a liking to Michael and grants him the title "Lovrina Fan Club Member No. 1".
-->'''Lovrina:''' I was so impressed by your toughness! Because you are so tough, I'll let you be the first member in my fan club! Doesn't that so make your day?
** Also, Gorrigan's letter talking of his new "friendship" with Micahel is so over the top that some can't wonder how deep these feelings of "friendship" really run.
* HilariousInHindsight: The Hexagon Brothers are obviously a ShoutOut to Franchise/SuperSentai. However, they beat Sentai to the punch with a purple/violet ranger - [[Series/JukenSentaiGekiranger 2 years]] before Sentai would have their first official one - and a brown ranger - [[Series/SamuraiSentaiShinkenger 4 years]] before a wannabe ranger would take those colors.
* ItsTheSameNowItSucks: Some thought the game re-used too much from ''Colosseum''.
* MoralEventHorizon:
** Cipher as a whole crosses it in the first scene (as if they weren't on the other side of the line already) with the destruction of the S.S. Libra, which is confirmed to ''kill'' several people.
** Individually, we have Snattle's imprisonment of an entire town's population (apparently using violence no less), Lovrina's corruption of Shadow Lugia, and Ardos attempting to get Michael and everyone else within the area killed.
* {{Narm}}: The title is hard to take seriously when it looks like the laughing {{Emoticon}}.
* NightmareFuel: The idea of Shadow Pokemon was already scary enough, but Shadow Lugia is a Pokemon so completely messed up its body literally transformed.
* ParanoiaFuel: Cipher Peons have a tendency to drop down from the ceiling when you least expect it. There's also one time where you get on an elevator alone, and you come out of said elevator with a Peon behind you.
%%* ReplacementScrappy: Michael is seen by many as a huge step down from Wes.
%%* TheScrappy: Michael's [[AnnoyingYoungerSibling little sister Jovi]].
* ScrappyMechanic:
** For many, Poké Spots defeated the entire point of Shadow Pokémon and Orre. Though each Poké Spot has three different Pokémon each to catch for a total of nine with three Poké Spots, and even then, three were necessary to trade for Duking's Meditite, Shuckle, and Larvitar, making it a total of just twelve different kinds by using the Poké Spots.
** The fact you lose any Shadow Pokémon you caught in a fight if you lose, unlike in ''Colosseum''.
* SpecialEffectFailure: The Bonsly Photo is obviously just official art of Bonsly plopped over a screenshot of Phenac City with a bad drop shadow.
* ThatOneBoss:
** Snattle's second fight isn't Greevil caliber, but it's also fairly brutal on its own, mainly due to his Shadow Starmie being a decent sweeper and being fought a long way away from a healing machine on either end, but you fight the smartest grunt in the franchise right afterwards.
** [[spoiler:Eldes]]. His Shadow Salamence is a few levels higher than anything you've fought at this point, and it will steamroll anything that isn't a Shadow Pokémon. Not only that, but his other Shadow Pokémon hit quite hard as well.
** Greevil not only has access to the three Legendary Birds, but also Lugia, as well as three Pokemon that are fairly strong in their own right.
** [[spoiler:Ardos]]. Unlike the previous enemies before him, and even a few after him, he introduces some diabolical shadow moves with three very high quality shadow Pokemon, two of which are fast, and have full movesets, the other, a Snorlax carrying Leftovers, being very difficult to capture. Oh, and his [[spoiler: Alakazam]], which he previously used to ''obliterate'' an earlier boss, will tear apart an enormous variety of Pokemon, covering all of the weaknesses of his team.
* TheyChangedItNowItSucks: Some fans feel like changing Orre into a much more habitable place made it lose its "edge."
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