Broken Base: The new soundtrack for the PSP release, done in the same style as the post-Persona 3 games. Some people aren't fans of the change and preferred the somewhat moodier soundtrack of the original. Oddly enough, many of those tracks ARE in the PSP version with some great remixes to them; but only in the Snow Queen Quest. If you have no interest in doing that quest; that's tough.
Grimies, purposely placed where they are in the final dungeon to make you risk the 40 minutes it takes to actually reach the final boss in one fell swoop. They are also The Unintelligible (literally, their words are numbers and deciphering them is a pain), which means that they're hard to negotiate with.
Any demon capable of spamming multi target ailment attacks like sleep and guilt, such as Nightmares and Arpachis. Imagine being powerless and mesmerized to attack each other.
The above is remedied by equipping personae which reflect or null their magics, but the trope is still upheld due to the rarity of those personae, plus the need to move onto better, more capable personae.
What's even worse is those who only put status effects on you and nothing else. It's actually possible to have to manually turn your game off due to getting stuck in a loop against some enemies.
Kuchisake-Onna is extremely hazardous against those who do an SQQ max Ambrosia run, in which the gamer at level 20 has to go into Thanatos Tower first. In there, she's commonly fought, she can't be talked away (easily), and she spams Mamudo, which will most likely off any member not fortunate enough to have a dark type persona, which at that point in the game, is extremely limited.
The toilet demons!
Ear Worm: As with the other Persona games from 3 onward, the PSP version has incredibly catchy battle music in "A Lone Prayer". Unfortunately, due to the game's high encounter rating, it can become Most Annoying Sound.
Following her return from Shin Megami Tensei if..., Tamaki Uchida has become this. While she's nowhere as strong as she once was, she proves her worth with the amount of knowledge she retains from her days at her old high school.
Among the Personas there is Vishnu, the ultimate persona of the Emperor arcana. Despite Amon Ra being the protagonists ultimate persona, it is Vishnu that is frequently treated as such instead. Even official material get in on it, with Vishnu appearing in art and the covers whereas Amon Ra doesn't even have official art in his Persona design, a sprite is all he's got. Finally, in the manga adaption, Naoya receives Vishnu instead from his other self while Amon Ra is absent.
Fridge Horror: Avidya World. It looks like your typical final boss dungeon, with creepy music and dark, distorted halls. But if you look at the doors closely enough, you'll notice that Avidya World is a twisted version of your school. And nearly all the doors of the "normal" school refuse to budge now...
That's because Avidya World is essentially Maki Sonomura's brain housing her worst inner demons mixed with the school dungeon layout. It's fitting on a thematic level.
"Mark danced crazy!" is the only thing kept from the horrid translation in the remake. Truly the "spoony bard" phenomenon of the 21st century.
And the silly password Elly recites to get back inside the school ("Roses are red, zombies are blue, but my face is white, so you know I'm true"), which has been improved greatly by changing the third line to "...but I don't want brains...", since Mark wasn't white in Revelations.
Brown: "You can make a tofu taco, a tofu burger, but you can't make a tofu cow!" What?
Personas of the Fool Arcana are relatively rare, with only three in this game and all available solely through fusion accidents. As of Persona 3 onwards, the Arcana is reserved for the protagonists and the Social Links associated with the Arcana are that of their teams. One of these Personas, Narukami, is associated with Electricity in the other installments of the SMT franchise it appears in and shares its name with the initial English rename of Elizabeth's Electricity spell El Jihad, which was renamed back to Jihad in Golden more than likely because P4 The Animation cemented the protagonist's canon name as Yu Narukami, whose main Persona Izanagi's spells generally revolve around Electricity attacks.
Magnificent Bastard: SEBEC Mikage-cho branch head Takahisa Kandori creates the DEVA system intending to use it to become God. When Kandori accidentally ends up manifesting Maki Sonomura's mind into the entire town of Mikage-cho, he manipulates Aki, the manifestation of Maki's rage, into trusting him and using Aki to reach his goal of becoming God. Getting resurrected to help with the plans of Nyarlathotep in the sequel, Kandori becomes one of the highest ranking members of the New World Order despite his lack of interest in advancement. When confronted by the heroes, Kandori allows himself to be beaten so that he may "experience" death, graciously accepting his fate. A mere human who managed to become a God because of his own intelligence, Kandori stands out as a true genius in the Persona franchise and is easily one of its most diabolical.
Narm: In the PSP remake, it sounds a little like the characters are flushing a toilet whenever they summon their personae.
The Scrappy: Tadashi Satomi, Author Avatar of the writer of the same name, is heavily disliked due to being lazy and primarily existing as a self-insert love interest for Tamaki, who is based on an idol the real Satomi admires named Yuki Uchida.
Scrappy Mechanic: Battles take place on a grid that determines which enemies you can target with which moves, and vice versa. This drags fights out longer than they need to be, as moving a character takes up their turn, and the odd targeting patterns of most weapons means that you may have only one or two characters capable of hitting an enemy, so you'll either have to pass a lot of turns and take hits or use up valuable SP.
The Experience system works on merit. The more work/damage you did in the battle, the more EXP you'll gain. This will catch a lot of players off guard at first when they realize Masao, the sluggish member of the team is suddenly five-six levels behind everyone else. Proper mastery of the fusion system (or simple counterbalancing a persona/character's strengths and weaknesses) will alleviate this to an extent. Regardless, it can be rough when this happens and you need to grind up your other members for negotiation purposes.
That One Attack: Pandora's first form has "Paralyze Puncture", a move that has a high chance of inflicting paralyze on the entire party which will result in a Game Over, making it essentially a One-Hit Kill. If the player is unlucky enough, she can use this on her very first move.
They Changed It, Now It Sucks!: The PSP version switches up the chest items by removing their original items and replacing them with booby trapped chests. Those who played the PSX version beforehand were irked by how many useful weapons (some of which were found from the Casino if the player didn't know which personas to refine) and items were taken out just so Atlus can mess with the player. They're also just a nuisance. They may drop HP to 1, but you have Mediarama really early which makes it a non-issue.
What Do You Mean, It's for Kids?: The initial release received a K-A rating (equivalent to an E rating today) from the ESRB, bumped up to a T rating for the PSP re-release. The original translation had a fair amount of swearing while updated localization has more of it, and both versions of the game feature high levels of sexual innuendo and nudity, including the final boss appearing to have a penis that makes up half its body.
Woolseyism: The PSP script compared to the original North American release. Atlus' NA localization team goes to great lengths to grasp every last nuance of characterization and mythology.