Antidote Effect: Averted. Even if both party members receive purify (or equivalent spell), these spells expend the limited magic that you have. There are also items that prevent status effects from landing if they're in your inventory.
Chest Monster: These also qualify as Paranoia Fuel. You never know when a chest in a dungeon is going to yield a nice item, or a monster that will kill you outright in 1-3 rounds. The first one you meet will kill you unless you know exactly how to handle it (and you will need a defense-up item just to stand a chance). So will the second, and the third. Oh yes, and after you've become strong enough to handle them, the game introduces red ones, and then once you can stand up to those, blue ones. This last variety actually use boss music. Oddly enough, the blue ones still come early enough in the game that you will eventually become strong enough to eat them for breakfast, and there are no stronger varieties.
Chronic Backstabbing Disorder: When you get certain Runes, there's a chance that your ally will betray you and try to take the Runes from you by force. Lejes is the ally which is most likely to betray you, while Esuna and Lux never will.
Crystal Dragon Jesus: Due to Nintendo's censorship policy at the time, the game' dialogue really dances around the issue, but Saro is meant to be God (or his equivalent) with Gorsia being his Crystal Dragon Satan counterpart. This makes Lemele and, by extension, the player character into a literal Crystal Dragon Jesus.
Fake Difficulty: The game (or at least the American version) practically is this, since the difficulty largely comes from insufficient stat boosts when you level up. Also, if you chose Esuna or Lux as your main character, you'll have to take a ferry to the northern continent. You get dropped in an area with monsters 7-8 levels above where you're supposed to be. Hope you can outrun them.
Duel Boss: Even if you have a second party member, whenever you fight one of the other apprentices, you have to do it alone. (Sometimes, if your main character is dead, they'll be willing to duel your ally instead of you.)
Guide Dang It: The apprentice you fight for the Star Rune is pre-determined as soon as you show the Wind Rune to the sage at Eygus. Whoever you fight for the Star Rune is Lost Forever. If you want that person to be your ally in the rest of the game, they must be in your group before you exit the Melenam Ruins. The game makes absolutely no hint of this whatsoever.
Hoist by His Own Petard: Carrying a Mirror in your inventory has the hilarious effect of petrifying the enemy that cast it on you in the first place. Most monsters that cast Petrify are not immune to petrify. This can easily turn an Oh Crap moment into an LOL moment.
Incendiary Exponent: Wilme attacks monsters by setting his arm on fire and punching them in the face.
Level Scaling: There are points where you fight other playable characters as bosses, and they are matched exactly to your level. Also, if you lose to them, they'll take your runes, making the inevitable rematch that much harder.
In the US and EU versions, the player character has very limited stat increases compared to the Japanese version, but the apprentice opponents retain their original high stat increases from the Japanese version. That means that the apprentice opponents get exponentially stronger than you as you level up.
Lost Forever: Any apprentice you get in a fight with can never join your party from that point on. If you want them in your party, you really should make them your partner in Bonro or Zellis (the third and fourth towns in the game), since they are far more likely to pick a fight without asking in later towns, and the one who gets the Star Rune will fight you no matter what.
Luck-Based Mission: Pretty much the entire game, really. Because many enemies can one-shot you just by using the right (or wrong, depending on how you look at it) attack, there are very, very many situations where your only hope of survival depends on how generous the Random Number God is feeling.
Master of None: Kamil. Intended as a Jack-of-All-Trades, the stat growths bug leaves him worse than everybody at almost everything. Literally the ONLY two people he beats at ANYTHING are Lux and Wilme in MP and Valsu and Esuna in Power. Lejes or Olvan are better jack of all trades than Kamil is, due to having better growths and a better spell selection.
Multiple Endings: Oddly not present, even though you have a choice of characters who allegedly have different personalities and motivations.
Considering the ending, this is almost justified. Since the character is part of a stable time loop, they were essentially destined to end the game by reincarnating, with the actions and history of their reincarnated self predetermined.
The game is all about Forced Level Grinding and making suicide runs to the towns selling the best equipment. If you do enough of it, even that Manrot that has been killing you again and again and again will seem feasible in a couple levelups. Gain another 2-3, and you're wondering why you were ever afraid of those guys in the first place. Make a Suicide Run to the next town to buy the newest set of armor/weapons, and come back. You'll be eating them for breakfast.
Peninsula of Power Leveling: Since the game splits XP between the Hero and his buddy, you will level far faster solo than you would with an ally. When you do recruit a new ally, their level is equal to yours and their equipment is appropriate for your level, even if said equipment is not normally obtainable yet. If you already have an ally, just let him die so you can earn all of the XP. When done, get a new ally, and the old will happily rejoin you with enough Save Scumming.
A better example would probably be the Isles of Beore (where Luze is located) due to its infestation of S. Brains, though it's more of an Island of power-leveling.
Plot Coupon That Does Something: Each rune has a special power when used in combat, from boosting stats to healing health, and can be used an infinite number of times.
Random Encounters: Sort of. You have a crystal ball that allows you to detect monsters. In theory, you can dodge them and avoid combat. In practice, the monsters move through walls, and are fast and numerous enough to hunt YOU down.
Prophetic Names: Never give your civilization-changing project to a man named Dr. Fail.
Suicidal Overconfidence: Averted, annoyingly so. Many enemies love running away, especially while you do your Forced Level Grinding. This is especially annoying when you're trying to kill the silver brains, and you have one almost dead and it runs away.
Underground Monkey: As in nearly all Role Playing Games of the era, many enemies are just palette swaps of earlier enemies with higher stats and maybe new powers. This even happens with a boss: Pison becomes Red-Pison (seriously, that's his name) and finally Metal-Pison.
Unusually Uninteresting Sight: Nearly all NPCs will act exactly the same regardless of which character you play as, even if you happen to choose Lejes the demon, Lux the Tetujin, or Wilme the alien.
Occasionally Averted, especially with children who think that the Tetujin is really, really neat.
Unwinnable: Don't fight Valsu after level 40. Also, make sure your levels are in the high thirties before fighting Gariso, and that you're well stocked on B Protects. Trust us on this one.
Useless Useful Spell: Averted. Petrify, Defense2, Vacuum1, and Vacuum2 are all very useful, due to how hard normal enemies are.
Some enemies appear to be weaker to these attacks than others, apparently based upon some sort of intelligence/magic defense stat. Some enemies are notoriously vulnerable to it (those tall fire guys are a Peninsula of Power Leveling to anyone with Vacuum 2), while others, Vacuum almost never works (Sages and Brains).
We Can Rule Together: The apprentice who takes the Star Rune will make you this offer, and you can even take him up on it. If you refuse, you fight immediately. If you agree, the front door of the castle will be unlocked so you can go heal up and skip the trek through the dungeon before the battle.