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.
YMMV: Shin Megami Tensei II
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 Rush 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.
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. (And also possibly one of the things that kept and continues to keep the game out of America, given how it would go over here.
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.
Hilarious in Hindsight - The Puck subquest, in which Daleth tries to screw you over with Infidelity 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.
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.
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.
Unfortunate Implications: While Word of God might say that YHVH being blatantly evil is merely a sign of worse things in the universe, the content of the game itself really ends up feeling pretty aggressively anti-Abrahamic, if not at least anti-Semitic due to just how much the Messian stuff draws on (non-Biblical) Judaic lore on top of Christian imagery. There's a grand total of one sympathetic Messian consistent to all paths, that being Gabriel, and with Zayin being so on Law where he doesn't completely lose himself to Satan and realizes that YHWH must be stopped; everyone else involved with YHVH and the Law alignment is incredibly evil and must be dealt with, no matter which path you are on, including Law. Yes, you have to fight YHVH even on the Law path!
The real back-breaking straw, however, might be the sidequest where you have to go around freeing the Shinto pantheon from imprisonment, which culminates in Amaterasu herself going on a fairly lengthy rant about how the vain, grasping "Hebrew gods" (literally Hebrew gods, straight from the Japanese script, not an invention of Aeon Genesis) tricked some of the kami into locking others up and then turned on the conspiring kami themselves. To anyone outside of Japan, it comes across really uncomfortably.