Well, I'm probably going to repeat some that have already been said...
The World Ends with You: It's...complicated. The main character starts off "emo", but kinda outgrows it over the course of the game, and the various villains are either power hungry, start off "emo" before changing, or are just trying to create a utopia in their eyes...Or they're just tricksters. It's a veritable mishmash of gambits and motivations.
Etrian Odyssey 3: The "optional overpowered secret final Eldritch horror boss that's actually behind everything" just wants to consume life because "that's what it does", and the monster subspecies it created just want to consume and control because that's all they know, and the one that started their race wants them to keep doing it. And then you get into the whole dual-faction story and how tragic it is (No seriously, it's freakin tragic if you do either of the two factions' final missions) unless you manage to find the third option near the end and just kill off the thing leading the monster subspecies. Best story in the series, hands down. Intrigue up the wazoo river, and lots and lots of tragedy.
Etrian Odyssey 4: Dude just wants to save his home kingdom from starvation and death, and has literally no qualms about committing genocide in order to do it. Optional secret boss is just a failsafe mechanism that went wrong.
Xenoblade: Can't exactly say without spoilers, but no, nothing to do with "Emo". Just pure unbridled arrogance.
Final Fantasy 4: Genocidal lunatic wants to wipe out existing civilization so that his own civilization can take over that land for themselves.
Persona 4: Can't say without spoilers, but no, no emo here. Again, it boils down to arrogance.
And there's also my own RPG that I made, where it's just a tyrannical queen who just wants to take over the continent she's on. Oh, and you work for her as she sends you on a near-suicidal assassination mission. (Don't wanna get flagged, so if you're curious and want a link, PM me)