Darkness-Induced Audience Apathy: When the world slowly grows more and more crapsack and the canon route involves murdering nearly everyone do you honestly think any of the characters deserve to win? Then again it could be Fridge Brilliance to show that even the Neutral path can be just as bad as Law and Chaos.
Ensemble Darkhorse: Alice's first appearance is in this game, as a minor character who exists solely to provide motivation to a couple of side villains, and doesn't even fight. She was so memorable that she's been brought back numerous times and is usually depicted as being very strong.
Zio's many forms stun almost everything in the game. With high enough speed, the heroine can immobilize pretty much everything before it even has a chance to move. The Bufu line of spells works just as well, but you need demons for those.
Marin Karin and attacks with similar effects are even worse. Most enemies, including bosses, are capable of being enthralled, and will then for the next few turns keep hitting themselves (compared to the one-round stun of Zio, that's quite the upgrade).
Not too long after the game begins, at one point you come home and, naturally, visit your mom. What seems like typical mother-son banter takes a turn for the worse when she starts speaking haltingly while coming off as extra-affectionate towards you. One of your allies warns that this is a sign of something weird. He's right; it's actually a demon in disguise. A demon that had just eaten your mother. You then have to avenge your mother's death and whoop his ass.
No matter what route you take, both of your best friends will die. On Law and Chaos, you have to kill one of them yourself due to opposing alignments, with the one you aligned with dead either from an artifact too strong for him or from your other best friend who had become his enemy. On Neutral, you have to kill both, because they refuse to accept anything short of full Law or full Chaos.
The extreme encounter rate. This is a game where you can get into fights with demons inside a bustling shopping center. The iOS version tones the encounter rate down, making it you don't get into fights every three steps, at least until you hit the End of the World, in which the encounter rate skyrockets back to the originals infuriating degree,
Trying to use the map. Summoning the map screen requires two layers of menus, and the Mapper spell, which provides a handy minimap, requires three, as well as 2 MP, and it doesn't always work. Hence why the sequel allows you to enter the map screen simply by hitting Select (not to mention it's easily selected using the L-button in the iOS port).
"Seinfeld" Is Unfunny: The game was truly revolutionary in its treatment of the post-apocalypse, demons, morality and the like... and everybody in Japan proceeded to rip them right the hell off, from Neon Genesis Evangelion to Super Robot Wars to Soul Eater (the latter being a kind of Lighter and SofterDeconstructive Parody, that's how far we've come). Seeing what made the original game so unique can be somewhat harder in this day and age. The gameplay also suffers from this in a huge way - in 1992 the first-person dungeon crawling was relatively unique in execution. For anyone used to post-Quake 3D navigation or PS2-era and beyond user interfaces, though, the game will want to make you tear your eyes out in frustration over how clunky it is. The mapping feature itself requires you to open two menus alone.
The Playstation version lessens the gameplay element of this a little, with interface improvements and graphical upgrades.
The years have not been very kind to the game as well, the game's combat and leveling up are pretty bare bones compared to Nocturne's.
That One Sidequest: Want to get those Game Breaking weapons from the Fiends? Good luck finding them, as they appear in certain areas with 1/256 chance of them appearing, with the weapons appearing with a equal 1/256 chance.