* 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:
** The backstories behind Eevee and Togepi. Awww!
** 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]] is the most remembered thing about this game, and even to this day there are several fans demanding that it makes another appearance in the series.
* FanPreferredCouple: [[ToyShip Michael]] [[FoeYay and]] [[EnsembleDarkhorse Lovrina]].
* 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?
* ItsTheSameNowItSucks: Some thought this game re-used too much from ''Colosseum''
* IThoughtThatWas: No, the name of the game doesn't mean "Pokémon, LOL".
* 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}}.
* 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 [[MemeticBadass 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''.
* ThatOneBoss
** Snattle's 2nd 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 steamroller 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, Snorlax, having 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: The things they ''didn't'' keep the same rubbed some fans the wrong way, particularly changing Orre into a much more habitable place, thus losing its "edge."