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.
The Subjective Tropes have appeared. It's the killer. Do not die.
Concerning Catherine: is she a malevolent entity who has willingly led several men to their deaths at the behest of Mutton? Or is she merely a Punch Clock Villain who has found someone she genuinely likes in Vincent?
Vincent, Johnny, and Orlando make it pretty clear that they don't want Toby dating Erica, but are they trying to protect Toby from sleeping with a transsexual? Or are they trying to protect Erica from becoming the victim of another hate crime?
Base Breaker: Erica, good God. Many people were riled up by the fact that she is a transsexual and how she's treated.
Katherine also has shades of this, due to some of her actions. Speaking of which, Catherine has shades of it, too...
Disappointing Last Level: The last few stages introduce Random Blocks and Monster Blocks, making the stages less about puzzle-platforming and more about undoing until that next Random Block turns into the block you need.
"Hilarious" might be an overstatement, but some scenes become amusing when looked back on with the knowledge that Catherine is a succubus, and Invisible to Normals:
When Katherine showed up with the cake while Catherine was over, she couldn't have seen Catherine anyway... and when Catherine went into the bathroom, she was probably just eavesdropping from there and waiting for the most inopportune time to flush the toilet.
When Catherine showed up at the Chrono Rabbit while Vincent was there with Katherine, she was probably just hanging out in the entryway, shouting things in Vincent's direction.
It's Hard, so It Sucks: You know something's hard when the masochists that are the Atlus fanbase have so much trouble that Atlus had to patch in an easy mode.
Worse. There are nine stages of climbing, eight of which have these bosses. However, from a certain standpoint, Shadow of Vincent and Thomas Mutton/The Dumuzid are the worst. It's not just their designs that make them scary. In these "boss fights" these two are circling the stairway as Vincent climbs. Not climbing after him, CIRCLING him!! Now, it was bad enough for the poor guy when it had to outclimb the ones chasing him up. The horrible realization sets in that these particular foes are playing with Vincent. And it STILL gets worse!
Not to mention that Shadow of Vincent at one point turns the entire stage pitch-black, save for his creepy-ass grinning mask, and will kill you instantly if you don't climb fast enough. Oh, and then he eats another dream-climber, Steve, right before your eyes.
The Sheepmen. What happens after they die in the dreamworld. The looks on their faces, they even still got the sheep eyes.
One-Scene Wonder: Nergal, Catherine's dad and ruler of the underworld, only shows up in the good and true endings of the cheater's route.
Periphery Demographic: Surprisingly, the game's multiplayer mode has become popular amongst competitive gamers, to the point where in some locales, there is a tournament scene for the game.
Unfortunate Implications: There are some issues with the meter, which symbolizes Freedom/Order, not Good/Evil (as the game leads you to believe until the end). While some of the choices seem far less unfortunate once this is known, some... still don't. Rather sexist answers tilt you towards "Order", implying that a pro-marriage person doesn't really believe in gender equality.
That and some of the more Jerkass options push you toward "Freedom".
Erica, the spunky waitress. It's not her character that's problematic, but everyone else's treatment of her. Nobody seems to care that her boss is sexually harassing her, Vincent and his friends act derisively towards her for her female identity, and Toby is actively discouraged by others from pursuing her romantically, all simply because she's a transgender woman.
The idea that having sex with a transgender person is disgusting is played for laughs. Although it's hard to tell whether Toby finds the fact that she's transgender abhorrent, or whether he's actually upset because he was only informed Erica is transgender after he slept with her. Furthermore the fact his friends and more importantly Erica withheld this information from Toby, which they all seemed to know would end his interest in her, carries it's own negative implications.
Not to mention she mentions having the same dreams that the men have, because she used to be male, which sets up a Red Herring about the nature of the dreams. As opposed to her not having them because she doesn't identify as male in the first place.
The game's ideas about the sexual politics of relationships and marriage, which seem to be that women only get into relationships for the ultimate purpose of marriage ("It may be a one night stand to a man but to the woman it is the begining of a whole life together" to use the words of a certain someone) and men are immature manchildren who will do whatever they can to avoid this commitment, are also somewhat dubious. It also seems to believe that the only purpose of marriage is to make babies.
It should be mentioned that all of these are decidedly Japanese viewpoints and come across as very offsetting by Western audiences.
The Untwist: Catherine is a succubus. Who honestly didn't see that coming?
Why Would Anyone Take Him Back?: Justified! During the course of the main game, Katherine breaks up with Vincent for pretty justifiable reasons. So, since you can get a Katherine ending, there has to be a good reason why Katherine would ever take Vincent back...and lo and behold, it turns out Catherine was an illusion and Vincent never really cheated. Although it sounds like bullshit at first and Vincent's friends have to back him up for the explanation to stick.