The intro to the game simply has Neku explain how much he can't stand people in general. Basically, him yelling at a few people, then "I don't get people. Never have, never will." Doesn't really get elaborated on during the main story, but it finally gets an explanation in Another Day's Pork City quest: Neku blames himself for the death of his only friend.
This is actually hinted at in the main story, too: when Rhyme gets erased, Neku thinks, "I feel like crap. This is just like that time... That time? What time? ... I can't remember."
Anticlimax Boss: In Another Day, Shinji Hashimoto is quite easier than some of the previous Tin Pin opponents.
Anguis Cantus, despite looking awesome, is piss-easy. So long as you don't go Leeroy Jenkins and get wiped out by his headbutt, all he can do while you're on the ground is to use a slow and fairly weak fireball spread (with the occasional big one thrown in). Oh, and then there's his tracking bubble: but it actually works to your advantage to get grabbed, seeing as this lets you wail on him with impunity while he charges a very slow fireball, giving you plenty of time to ready a cross-combo.
Awesome Art: Needless to say, the graphics and general style of the game come out quite nicely, helping to make Shibuya feel like an ever vibrant world. Especially when looking at the iOS version.
Joshua. While he's a Jerk Ass who turns out to have killed Neku and essentially manipulated him to "win" the game against Kitaniji for him so that he could erase Shibuya, a lot of people find him endearing.
Ear Worm: All of the soundtrack is pretty catchy, but Calling will gorge its way into your head for days.
Escapist Character: Hanekoma. He's always two steps ahead of everyone and both God and Satan but, mostly because of keeping in the background of things, he manages to keep a sense of mystique and interest to keep from being obnoxious about it.
Fanon: The concept of a "Music" of Shibuya is widespread and largely accepted with no explanation in fanfiction; it's never even alluded to in the game, though it does make some sort of sense and fit with the musical theme naming (Noise, Conductor, Composer, frequency, etc). Plus most of the Noise are named after music(Dixiefrog, Pig Samba, Neoclassical Drake).
Fountain of Memes: Pick Sho Minamimoto's out loud quotes. Any of them, and fans of the game just might start having quote-offs or break out into math speeches.
If you use Mingle mode and come across another player doing the same, you can access that player's shop, which consists of what the player's characters were equipped with at the time. Through this, you can, early on in the game, buy pins that you normally wouldn't get for a long time, such as the Anguis and the Darklit Planet set, and quite easily demolish every enemy that comes your way.
And of course the LASS thread set, short for "Lapin Angelique Suicide Special," which uses threads which require the SOS condition. The correct set of four grants an insane level of offense and defense, often meaning 0 damage on the user and high amounts of damage to the enemy. There's even pins and threads which automatically inflict SOS at the beginning of battle. Combined with the Darklit Planets, any enemy you face is... pretty much SOL.
Neku and Joshua's Level 3 Fusion Attack. It can be used to basically skip the Nintendo Hard Phase 2 of Sho Minamimoto's boss fight by taking almost half his HP off. To put that in perspective, Shiki's level 3 Fusion has an Efficiency rating of 20, Beat's has an Efficiency rating of 30, and Joshua's level 3 Fusion has an efficiency rating of 99.99.
The Solo Remix edition buffed Lightning Arrester-type pins (like Lightning Rook) with more hits and charges, and is now comparable to the Darklit Planets in damage. Even better, Lightning Rooks are much easier to get, plus you can equip two of them and still have four pins of your choice (unlike the Darklit Planets which takes up all your slots).
Some of Minamimoto's references are just random math terms thrown around for fun, but then there's the Level i Flare...
And the HP count of both his forms in the Noise Report... but this one should be easy to get, considering how he recites Pi in-game.
Also, there's a Japanese Culture Genius Bonus: In Another Day, when Beat is trying to become a comedian, it's just plain funny. It becomes funnier if you know that there is a Japanese comedian by the stage name of BEAT Takeshi.
Though bats in this game aren't really goddamned so much as Frogs (especially if you use Joshua's floating move) or Shrews (who use bombs and drill attacks for massive damage, and on top of that burrow underground, making them difficult to attack).
Later, you encounter Frogs that absorb either short-range or long-range attacks. Or a particular kind of frog that absorbs both.
This frog that absorbs both get VERY special notice. You can only fight them in the Shibuya River areas in Another Day, and they're rare. Oh, did we mention that they're one of six enemies in the game that drop a Darklit Planet pin, meaning you need to fight them on Ultimate and chain a lot of battles?
Wolves, due to their almost-constant dashing.
Pork City has battles that pair these attack-absorbing frogs with the ELEPHANTS.
Ravens tend to be this too. The big raven boss, Cornix Canor, is very representative in that it stays off screen for 90% of the time and just decides to stop by every once in a while, flying past your silly attempts at hitting it.
Any Taboo Noise, because they're stronger, require you to pay close attention to the Light Puck if you want to do any decent damage, and actively seek you out during a Scan. Additionally, the 'Gotta Bounce!' option is disabled during their battles, so you can not escape them.
Not to mention the jellyfish. They multiply endlessly. If you try to get the red jellyfish's Hard drop by waiting for it to spawn, the battle can easily take up to 10 minutes just because they spawn faster than you can finish them off.
Towards the end of the final week, you'll occasionally and randomly fightbrainwashed Reapers as you go from one area to another. The encoutners aren't particularly hard so much as time-wasting.
It doesn't take very strong slash goggles to see several of the male shop keepers crushing on the player as hard as the females when you get their Friendship up — the le Grand clerk in Cadoi City's offering to help the player slip into his purchases being the most explicit. He will drop several sexual compliments on the party as they shop — however, there's only a one-third chance that there's even a girl in the party, meaning two times out of three he's hitting on a pair of fifteen year-old boys.
There's also a fair amount of Les Yay, too — Shiki's most important character arc is her relationship with Eri, while Mina and Ai seem to care much more about each other than Makoto...
It's even lampshaded in the bonus chapter at the end of the game, where Joshua's codename is 'Pink', someone comments on how a Rainbow Tin Pin Launcher was 'made for him' and he's the 'Roy G. Biv' of Tin Pin, and Josh himself offers to escort Neku alone down an abandoned drainage river and "spend some quality time". Shiki is torn between shock and Yaoi Fangirl-ism.
Hype Backlash / Internet Back Draft: Square had a week-long countdown with loads of promotion for...announcing an iOS port of the game. Fans and the media, expecting a sequel, were not terribly amused.
Magnificent Bastard: Joshua and Kitaniji arguably qualify since their plans both failed and succeeded at the same time, but Mr. Hanekoma is the crowning example of this trope. Just read the Secret Reports.
Must... resist... emo urges! Explanation "Another Day" presents us with a considerably more upbeat Neku, whose love of Tin Pin Slammer prevents him from being the antisocial jerk he is at the beginning of the main game.
There's a party in my mouth! Explanation Beat says this if you give him food he really likes
Feel me when you come inside / Touch me when you want me anytimeExplanation Many players have noted that "Give Me All Your Love" has some surprisingly explicit lyrics for a T-rated game, with these two lines being the most blatant in their sexual content.
The Game Over sequence. The music suddenly stops, Neku whispers, "I-I'm fading..." in a horrified voice, and then both screens turn to static. It's even worse when you're fighting Game Masters, as they'll make a snarky comment too.
Sometimes, it'll be your partner who speaks when you die, and their death cries can get pretty horrifying. Like Beat, who, instead of whispering like Neku, screams"RHYYYYYME!" That one's more of a Tear Jerker, however.
Player Punch: Several. The first one (Rhyme's erasure) gets pulled surprisingly early, and it's far from being the last.
Polished Port: The iOS and Android port is a really good single screen translation of a dual screen game, and has updated visuals. Along with that, there's also the Sequel Hook during The Stinger.
Replacement Scrappy: Joshua inspires these reactions. As a character, he's quite a jerk, to put it mildly, while Shiki was, in spite of her own insecurities, a Nice Girl who could call out Neku on his more jerkish behavior. As a party member, he's quite difficult to use at first, particularly since he doesn't have his Game Breaker aerial combo yet, while over the past several days, you've likely acquired some useful upgrades and a good set of clothing for Shiki.
Scrappy Mechanic: It seems like eating food to raise your drop rate should have no detrimental effects; after all, you're only raising your likelihood of getting pins, right? Well, there is one kind of situation where having the drop rate increased is actually bad: the boss Time Trials, including Final Time Attack. Waiting for dropped pins to spiral to your characters counts towards the time taken to defeat a particular boss — about one or two seconds, to be more specific. Even a run at level 100 will yield a good chance of randomly slowing you down with pin drops if you ever eat any drop-rate-increasing food. There's no way to undo the effects of stat-raising food, so unless you start a new file, kiss your serious attempts at record times goodbye.
Konishi can be rather difficult as well, since she's a very confusing Puzzle Boss who can easily destroy you if you can't figure out exactly what you have to do just to scratch her. The solution is implied before the start of the battle, but it isn't explicitly stated and requires you to do things that you would not have thought about before.
After Konishi, you fight Kitaniji. He has the highest HP of any enemy of the game thus far (though Wooly AOR ties him) and has extremely powerful attacks. Not to mention his main ability. And brainwashed Shiki makes it rather hard to attack her, and blocking Mr. Mew completely is hard.
Uncanny Valley: The character designs for some of the younger characters (particularly the main cast) are pretty damn skinny (especially noticeable Shiki since she shows the most skin) compared to Nomura's other designs, which some people have noticed. When the cast makes a cameo appearance in Kingdom Hearts, it becomes especially noticeable (and again, Shiki still stands out) when you can compare Neku and Sora's physiques once they meet one another.
It's really not that Rhyme is unfeminine; if you know that she's female it's perfectly easy to see. It's just that a) they don't give you an indication of her gender until pretty late into the game and b) one is so used to seeing Bishōnen who look even girlier you just assume it's a boy.
She's also only twelve, so she could just be a late developer.
The Woobie: All of the main characters have their moments of being this.
Shiki has self esteem issues (to the point she took on Eri's body in the Reaper Game, only to realise this made her feel worse) and feels very guilty over the fact that she's jealous of her best friend.
Beat accidentally got himself and his sister killed and is beating himself up about it, then tried to revive her by joining the Reapers only for Konishi to crush her Noise form. Plus he's The Unfavourite to Rhyme and constantly mocked by enemies (and sometimes other players) for being an idiot.
Rhyme dies three times. First when she and Beat are killed in a car accident, then when she performs a Heroic Sacrifice to save Beat from a Noise, then again when Konishi crushes her as a Noise. It's also implied that her payment for entering the game is all her hopes and dreams, and the secret reports claim that they'll be lost forever since she didn't make it to the end of the week.
Even Neku and Joshua can be seen as this. The former is implied in Another Day to be anti-social because he believes he got his friend killed since he asked the friend to come over and he was knocked over by a car as a result, to say nothing of everything he goes through in the game. The latter is hinted in the secret ending at wanting to be friends with the other players, but being unable to.
Woolseyism: The game is just about made of them. Example given: Beat's rough, tough-guy speech patterns in Japanese were changed to Ebonics for the English version.