These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Bai, who is weak and will rob and desert you if you stay at an inn.
Clay, while a decent fighter, annoys players with a dungeon fee even in "dungeons" with no monsters. If you refuse to pay him for any reason, he'll act rude and leave you.
That One Boss: Boozoo. He has tons of hit points and can hit with you with Rapid-Fire Fisticuffs that can potentially hit the whole party for heavy damage. The worst part: you have to fight him twice in a row.
Why the heck Chezni is now bald and calling himself Petro, in addition to Midia and Daphne looking completely different.
The hints that Chezni had stolen the throne of the Potentate through a bloody coup.
These two did have something of an answer in the game. One random townsperson you meet claims to have been the king, but no one remembers him. it's likely the coup wasn't bloody at all, but rather based around Laser-Guided Amnesia. Chezni's baldness may also be to hide his Raigan heritage. As his blond hair was pointed out as unusual for a Lafury at one point in the original game. The latter two still don't make sense though.
Why everyone on Eltz knows about Chezni and Midia, and worships them, despite them apparently trying to hide their identities.
The Great Union in general.
Granada's entire motivation.
Values Dissonance: The... "humor" found throughout the game. Does any game really need that many jokes revolving around "Ha! Women!!"? Not to mention the number of sidequests which are resolved by the beating of either children or spouses.