* EpilepticTrees: Apart from being [[spoiler:defeated by Flay]], what set the Light Mana against the concept of humans and Mana living together is [[spoiler:a Mana dying from childbirth in a relationship with a human.]] Here is where the WildMassGuessing comes in: [[spoiler:''Pepperoni'' is the child of the human-Mana union.]]
* GermansLoveDavidHasselhoff: In Japan, the two ''Mana Khemia'' games received a fairly lukewarm reception from the established fanbase, and ''Mana Khemia 2'' received a lot of flak from reviewers. In the West, however, it was much better received (and reportedly sold ''better'' in the West than it did in Japan). ''MK 2'' also got a ''much'' warmer reception from the Western press than it did in Japan, scoring slightly ''higher'' on average than ''MK 1'' did.
* HoYay:
** Pepperoni and Goto are uncomfortably chummy with one another for most of the game, despite Goto's repeated assurances that he "doesn't swing that way". Goto intentionally invokes this during one character quest, wrestling with Pepperoni and then chasing Enna around the library. Tons of innuendo are included. [[spoiler:It's a ploy to deter Marta from seriously pursuing Goto. It doesn't work.]]
** Yun and Raze as well, especially during the former's character quests in later chapters. There's also this exchange:
---> '''Yun:''' I have the day off, so I thought you might like to go out drinking with me.
---> '''[[HeWhoMustNotBeSeen Goto]]:''' I'd like that, but... what are your intentions after getting me drunk?
---> '''Yun:''' [[GoofySuit I wouldn't mind ripping that suit off you]].
* {{Moe}}: Puniyo, a 5-years old blue-haired girl who rides a giant Puni and [[PokemonSpeak speak like a Pokémon]]. Lambshaded by Lily, who has a Puni fetish.
* PlayTheGameSkipTheStory: While opinions differ on the Gathering Minigames, [=MK2=]'s gameplay is an improvement over his predecessor. On the other hand, most of the plot resolves around comedy routines and Flay shenanigans, and not even the Big Bad is taken seriously. Also, unlike the first one, this game lacks an interesting plot-twist to make up for it.
* ThatOneAttack: [[spoiler:Tetri and her PaletteSwap]] can disable the Support command, preventing you from switching characters and using the LimitBreak moves.
* ThatOneBoss: Kyobos, fought on both routes, has powerful moves that targets the whole team, like Tri-Fang (which also cause poisons everyone) and Hellfire (fire spell that can be a TotalPartyKill if you're not prepared).
* ThatOneSidequest: Some of the jobs from the Extra Chapter are alchemy requests with very specific Ether Levels. For example, creating a Gold with the ''Expensive'' ether effect requires a [=EL=] between 84-85, a riduculous short range. Since you don't want to waste ingredients, expect to do lots of SaveScumming until you get it right.
* TheyChangedItNowItSucks:
** The changes in the character quests. While the number of [=CQs=] per character remain the same, the events generally do little in terms of CharacterDevelopment and are more focused towards comedy, which reduces the VideoGameCaringPotential.
** The new item gathering format was [[ScrappyMechanic considered very tiresome]]. While in other games you would just slash or push a button, now you are forced to play minigames for each type of gathering action, except fruit and water gathering.
* TheyWastedAPerfectlyGoodPlot: Everything related to Flay's secret organization. [[spoiler:Then there is Flay's battle against the Light Mana.]]
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