Anticlimax Boss: The Twelve Shinshou. They are mentioned as early as during the first trip to the Abyss, and you start to mentally prepare for an epic Boss Bonanza that requires careful conservation of resources... only to find out that they're complete pushovers who die in 1-4 turns, have trouble consistently hitting your party and yield less XP than a Random Encounter.
Kuzuryuu is very important to both sides' plans and is the only Neutral exclusive boss in the game. He ends up being relatively easy compared to Lucifer beforehand and the Shinreis afterwards.
Anvilicious: The subplot about the poor Woobie Shinto gods being imprisoned by YHVH so no one can worship them anymore is about as subtle as a sledgehammer upside the head. It's a pretty strange anvil to drop, considering that the Shinto religion has always been exclusive to Japan and the number of Christians in Japan is less than one percent of the population even today. (Having Amaterasu Herself go on a bit of a tear about "grasping Hebrew Gods" gets a bit uncomfortable, to boot.)
Discussions over whether Neutral or Chaos is the "best" ending (Law is not an acceptable answer, even though you still challenge YHVH), and moreover which one the devs intended to be the best ending, can get quite heated.
Complete Monster: The twisted versions of Archangels Uriel, Raphael, and Michael are overlords of the theocratic dictatorship that has overthrown Tokyo After the End. Dividing the city into five districts, their Propaganda Machine claims they did so in accordance to the division of labor, but it is clear they favor the wealthy Central District and feel free to neglect, abuse, and slaughter outright the residents of the other four. When signs of rebellion appear in the Valhalla district, they order the Demon Lord Abaddon to devour it whole, promising to restore his angelic status if he did so; when he is finished, they cast him back into the demon world. The entirety of the Arcadia district has been lobotomized and plugged into Lotus Eater Machines, causing them to believe they live in an idyllic paradise while their physical bodies waste away; Aleph is subsequently informed the the Archangels intended to do the same to the entire planet. The workers of the Factory District have been brainwashed into slavery by the song of a Siren, who is routinely tortured by the Archangels' henchmen to keep her singing. Finally, they attempt to get Aleph and his comrade Zayin to surrender to them by holding the entire Holytown district hostage, threatening to cut off their air supply and slowly suffocate them to death. They don't even learn from their actions either, as their reincarnatedBonus Boss fights in Digital Devil Saga show they plan on doing it all again.
Crosses the Line Twice: Yes, Mara appears, but he doesn't have the Hurricane of Puns surrounding him this time. No, this game has Crowley/Master Therion, who holds Sabbaths to have sex with demons and, when forbidden to by Lucifer, complains about how horny he is and decides to kill you to calm himself.
This is the game that introduced Alice as an enemy. Also, while he didn't gain his popularity until the next game, this is also the game that introduced Matador.
This game's alignment representatives are Zayin/Satan and Lucifer. They happen to be among the most popular alignment representatives due to Zayin managing to defy the initial Lawful group and hold onto himself as he sinks deeper into Law and even managing to turn on YHVH in the Law ending, which most Law heroes either never do or only realize as they die, and this incarnation of Lucifer being a Well-Intentioned Extremist leaning heavily on the Well Intentioned side, to the point where it's this Lucifer most fans generally default to.
Game Breaker - No, not Zio. This time around it's damage and defense buffs and debuffs, which stack with themselves and last until they are dispelled, something that not every boss is capable of. But more-so is the Divine Retribution spell. It tears off a quarter of an enemy's health with an alignment opposite to the spell's caster, and it works on bosses with no reduction.
The Puck subquest, in which Daleth tries to screw you over with Infidelily Sap, and how it comedically backfires is funny by itself. However, when the reveal about Hiroko being Aleph's mom is discovered, it gets more hilarious when you realize Daleth got your MOTHER to chase him around like a lovestruck twit!
It Was His Sled: God (as in capital-G God) being the final boss on all three routes is one of the most well-known events of not only the game, but of the entire franchise.
Memetic Badass: Aleph is considered, along with the Demi-fiend, the strongest SMT protagonist. This most likely has to do with how the endgame of Neutral pits him against Lucifer, the giant dragon Kuzuryuu, three avatars of YHVH, Satan, and YHVH Himself.
Moral Event Horizon: YHVH ordering the total genocide of everyone not in Eden in the Law route. Satan is so horrified that his next target is YHVH Himself.
Michael, Raphael, and Uriel having Abaddon swallow Valhalla whole and later threatening to cut off Holytown's air supply. And if you do the Arcadia sidequest/Gimmel boss fight, you learn their ultimate plan: hook everyone up to a virtual reality to bring forth an artificial Thousand Year Kingdom, which also counts as an MEH crossing for the fully cooperative Gimmel.
Never Live It Down: It may not be an exaggeration to say that this game was this for God. While he's gotten more nuanced portrayals in later games, his incarnation in SMT II is what most fans default to when they think of YHVH.And then in Shin Megami Tensei IV: Apocalypse, it seems as if his portrayal in this game was so lasting that Atlus gave up trying to fix him, revealing that YHVH and the Great Will are not the exact same being. YHVH was so crazy that the Great Will was trying to stop him.
If you strongly believe in an Abrahamic religion, have fun trying to complete the game. Because at the end of the game is a twisted version of God as the Final Boss. Unlike in SMT I, where following Law means you side with him, in this game you still fight him, and just to drive home how terrible he is, even His angels want him gone.
Frankly, YHVH is pretty creepy even if you don't believe in him, as He's smack dab in the middle of the Uncanny Valley, giving you a perpetual Death Glare, and begins the fight with a rant about how you deserve to be tortured for all eternity (said tortures described in excruciating detail) for daring to be the good guy here. Oh, and if you're playing on certain emulators, the dialogue box constantly shakes.
If you followed the Law Route, you essentially support the eradication of all life on Earth. If you chose to destroy the Arcadia System Gimmel is in control of (Chaos), everyone hooked up to it dies, it's even worse if you take Gimmel's place by inputting your data (Law) since everyone who is hooked up to the System would die anyway cursing Aleph for letting them die.
One-Scene Wonder: Crowley and YHVH, the former for his out of nowhere hilarity (I'M SO FREAKING HORNY!) and the latter for what He does as the Final Boss and Big Bad, even on the Law route.
Seinfeld Is Unfunny: In the pre-Quake days, its pseudo-3D movement was seen as interesting and different. For any gamer who cut their teeth after 1996, movement and the interface will feel like chilled molasses. Even the inclusion of an auto-mapping system and a minimap producing spell can't quite help the confusion and slowness of 3D map travel.
Signature Scene: As mentioned above, the battle with YHVH is one of the most remembered parts of the entire franchise. While it's the least liked route, Law's version of it is probably the most well known, as Satan realizes the gravity of what just happened and calls YHVH out, proclaiming that it's time for the ultimate creator to be judged.
That One Attack: The last two bosses of the Neutral and Chaos routes and the Final Boss of the Law Route both have one hit kills they can use any time. Granted, they do use it on specific targets, but it's still extremely annoying.