Angst? What Angst?: After freeing Mikiko from the cell, Hiro reveals to her that her father is dead. It seems she doesn't care about him except for the quest about finding the sword.
Averted with the GBC version, where she doesn't take it well and she has a Heroic BSoD.
Awesome Music: The game's soundtrack stands in direct opposition to its gameplay.
Big-Lipped Alligator Moment: The miniboss fight with Cerberus becomes this in the N64 version. The Acropolis stage ends with a cutscene introducing it, only for the next stage to open with Hiro and Mikiko admiring a statue of Athena with no mention of the hellhound that just got skipped over.
Bile Fascination: At this point, the game's biggest selling point is based purely in its infamy. Common consensus is that this was the real reason the game was re-released on Steam in 2013.
Complete Monster: Kage Mishima is an evil CEO and the tyrant of a dystopian future. Discovering the Daikatana with his partner and its ability to time travel, Kage killed his partner and traveled back to 2030 AD, where he claimed the cure for a pandemic and sold it at a high price, leaving many people dead, while also making San Francisco a martial law town where gangs roamed the streets causing havoc. Becoming the iron-fisted ruler of the world, he forces his guards to go through brutal training, creates burgers out of human flesh, and regularly has his prisoners tortured and beaten to death, and uses his time travel abilities to assassinate members of the Ebihara clan. When Hiro Miyamoto refuses to swear his subservience to him, Kage tries to clash both of their Daikatanas together, knowing full well that doing so will destroy the entire universe.
Fight Scene Failure: Any time the Daikatana is used in a cutscene, expect it to be this due to the incredibly Limited Animation. A duel between Hiro and Mishima halfway through the game has the two halfheartedly swiping their swords at nothing.
Upgrade your jumping ability at all, and every jump you take will be accompanied by the distinctive sound from The Six Million Dollar Man. Remember too that late-90's FPS games were all about constant jumping.
Same goes for Power. Upgrades to this add a loud buzzing noise over your attacks, regardless of which weapon you're using. Worse is that upgrading this stat is vital.
The game is widely mocked as the "game were most of the enemies are robot frogs and mosquitoes". In truth, only the first couple levels have these enemies. Unfortunately, said levels are also among the most unpleasant parts of the entire game, meaning many players never make it past the first few levels before giving up, likely contributing to this misconception.
Polished Port: The Game Boy Color tie-in game released by Kemco somehow managed to be better received that the PC game it was based on. Sadly, it only came out in Europe and it was completely different in playing style to the original. However, John Romero put a link to the ROM on his site, so, fortunately, there should be nothing illegal about emulating it.
Porting Disaster: The Nintendo 64 version had blurry, low-resolution textures, and lots of fog to hide the shorter draw distance. The titular Daikatana was removed as a usable weapon. Mikiko and Superfly were removed from the gameplay (which actually makes the game more fun, but still) but remained in the cutscenes.
Protection from Editors: Even at a time when games typically had much smaller development teams with much more creative control, being a great game designer does not automatically make you a good project manager.
Scapegoat Creator: Zigzagged. The team that worked on the game apparently consists of one person - his name is John Romero. According to most people, he did all of the designs, all of the publishing, all of the marketing, all of the debugging, and as a result deserves all of the criticism. Still he was taking most of the credit, perhaps it's just Laser-Guided Karma. Or alternatively a way not to ruin the reputation of other people who worked on it. The fact that the most infamous piece of marketing associated with the game overtly asserted that Romero was personally going to, shall we say, dominate the gamer also didn't help matters, and even if he didn't think it up, Romero did okay it. Let's face it, when you go around claiming that the sole reason it's going to be good is because you worked on some other good games (Romero frequently talks like he deserves sole credit for Doom and Quake) and do most of the hiring and order the game to be entirely rewritten halfway through development, all while actively positioning yourself as the face and genius of the project the way Romero did, you don't exactly have the right to complain if everyone blames you when it all goes ass-up.
Scrappy Mechanic: The game originally required you to use "save gems" rather than allowing you to save whenever you want as most shooters do. The game also saves at level transitions, and rather annoyingly, they sometimes put save gems right near level transitions, making it likely you will waste the save gem in question.
Scrappy Weapon: So many, the vast majority of them being in the first episode. It's telling that one of the better weapons in the opening is the one that wastes six consecutive shots every time you fire it, simply because it's effectively the only ranged weapon from its time period that can't actively damage you like the blaster with bolts that bounce off a wall and back into you or the explosives that conspire with terrible collision detection to blow up in your face.