** 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.
* FanPreferredCouple: [[ToyShip Michael]] [[FoeYay and]] [[EnsembleDarkhorse Lovrina]].
* 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.
* 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, while not exactly ''hated'' per say, is seen by many as a huge step down from [[MemeticBadass Wes]].
* TheScrappy: Michael's little sister Jovi. ''Big time.''
* ScrappyMechanic: Poké Spots defeated the entire point of Shadow Pokémon and Orre.
** Though a Poké Spot had three different Pokemon 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 Poke Spots.
** 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.
** 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.
* 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."