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 anime as a whole. Fans either call it a faithful adaptation with some extra plot thrown in, or they call it another example of the dark side of The Anime of the Game titles, where it butchers the story by cutting out all of the fluff that makes it worthwhile as a game, as well as having the obvious cases of Off Model and editing certain plotlines to make them less suspenseful or humorous.
Creepy Awesome: Ameno-Sagiri and Izanami. They were scary enough in the game, but general badassery the cast displays, Yu especially, and to see them, respectively, almost outright stomp Yu without his friends saving him, and bring him to his knees while barely lifting a finger makes them even more frightening.
"We Are One and All", used in episode 25 when everyone attains their ultimate Persona, Yu fuses Lucifer, and they all defeat Ameno-Sagiri.
Ensemble Darkhorse: Aika Nakamura, a side character introduced in the anime, saw a sudden spike in popularity after a scene in episode 6 where she stoically delivers Chinese takeout to Chiein the middle of a chase sequence.
The rendition of the fight against Shadow Kanji in Episode 7. Were Yosuke and Yu homophobic and hateful assholes, or did they just not know how to handle such a situation? Was the scene supposed to be "OMG GAYS ARE FUNNY EW", or more like "DUDES DON'T BE STUPID, STOP BEING IDIOTS"? Another point of contention is that it was treated as much less serious than the other bosses, with the boys jokingly trying to leave Kanji to his shadow (compare to the game, where Yosuke still doesn't want to go in but puts that aside out of concern for Kanji).
The main character being renamed Yu Narukami in the anime (when he was known to some fans by his manga name of Souji Seta). Never mind that Yu Narukami is the canon name chosen by Atlus and the other was only made up for the manga, his canon name came second so therefore it sucks!
Signature Scene: The Investigation Team putting on their glasses against a stark yellow background in the second opening.
Unfortunate Implications: Episode 8, and to a lesser extent the game itself, has the scene where the Investigation Team are out camping, and they have to be split into a tent for the girls and a tent for the boys. This becomes incredibly unfortunate when both Yosuke and Yu tell Kanji that they're uncomfortable sleeping in the same tent as him due to his ambiguous sexuality, and their fears that him being gay would somehow make Kanji attracted to them and lead to him raping/molesting the two of them in their sleep. The entire scene is Played for Laughs. This causes Kanji to burst into the girl's tent, while leads to the hilarious scenario of him having to share a bed with an overweight girl. So not only is the episode homophobic, but they play the Fat Bastard trope for humour — we're meant to find it funny that he ended up in close proximity to a fat girl. While the girl in question is insufferably unpleasant in the game, in the animation she hadn't actually done anything to warrant the repulsed, disgusted reaction she receives — hell, she'd done them a favour by eating Chie and Yukikio's vile-tasting curry and liking it. The only thing she'd done by that point to warrant their negative reaction is... be fat. Also in the game, Yosuke is less homophobic about it, and Yu mostly just watches the scene unfold without comment.
Though it's suggested that something else happened between her and Kanji that night, to explain why he's so upset about it.