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.
Anticlimax Boss - You can't fight the final boss. All you need to do to "beat" it is to run away. Which will take you all of two turns. Yes, really.
Disappointing Last Level - Of all the islands, Nakiridani is probably the most entertaining, giving us a higly interactive environment, plenty of opportunities to learn about the people's culture, not to mention an original plot, and original setting. Later islands were much larger, had more generic settings, less interesting quests, and never really encouraged too much interaction with the people. By the time the player nears the end, the whole thing comes down to endless repetitive fights in Khamulon, and long, boring puzzles that do nothing beyond challenging the player's patience, in Umajo Kenta.
Game Breaker - Sira can paralyze any single enemy in the game with her Thorn Snare spell, including the final boss, making boss battles ridiculously easy. Her Frost Avalanche spell does this to every enemy on the battlefield (except bosses), reducing most battles to tedious rounds of ice breaking.
Sira is practically a walking Game Breaker — in addition to the above, she's actually almost as strong as Drirr, is one of the best ranged attackers, and her "Fungification" spell is by far the strongest single-target attack spell, more than thrice as powerful as Lightning Strike! (Its only disadvantage is that if it strikes the killing blow, the monster doesn't drop anything)
One of the late-game dungeons sports a trap that summons a horde of powerful demons to attack you. Normally, this is lethal to the party, but Mellthas' Demon Exodus spell, once properly leveled, can vaporize the entire horde in a single round. As the trap will faithfully conjure a demon horde every time you step on it, this process can be repeated indefinitely for massive experience.
Goddess' Wrath, once you power it to full. Can you say, "guaranteed instant death for all enemies"? Only downside is that it prevents you from looting their corpses, but you can only really use it for the final dungeon, so it doesn't really matter by that point.
Game-Breaking Bug: It's possible to get stuck in Frill's room after Drirr joins you. The bug seems completely random. Also, when entering a 3D area, seeing all 2D sprites (except people) scrambled means that the game is just about to crash. This too is completely random, but is likely to occur at least once per playthrough, and if murphy's law is any indocation, most likely after you've gone a long time without saving.
Good Bad Bugs - The Iskai healer in Jirinaar may randomly give you a healing potion as you end the conversation with her. The bug? You can do it as much as you want, making both a big reserve of free potions and a lot of money by selling more of them.
The infamous long reach bug will let you grab things that are just out of your reach, and you wouldn't be able to get them othervise. Picking up a fruit that paralizes ManEatingPlants? Snatching stuff from behind the counter and selling them back to the shopkeaper? Stealing a decent and expensive shield from a trainer, from across a stone wall? Sneaking into Kamulon without Khunag? Just right click as far as possible while moving towards them and you have it.
Inferred Holocaust - The author of the blog mentioned in the Let's Play entry had this take on the ending. You can see it below (though spoilers abound, obviously).
Most Annoying Sound - The bleeps coming from the internal speaker almost every time a bug is encountered. It's even more annoying when the bug is fatal (the game crashes and all unsaved progress is lost).
Nightmare Fuel - Dungeons. Just imagine those dark and clearly alien hallways with the sounds of water dripping, chains ringing, heavy doors opening and closing, animals howling, combined with eerie music and monsters growling and jumping out from behind the corners or just standing motionlessly and waiting for you to approach, not to mention the occasional magical or alien phenomena or complex mechanisms you come across every now and then which must all be figured out while dealing with these circumstances. And let's not forget the total darkness waiting when the lights go out.
Nailed it. The dungeons could have been the RPG equivalent of Silent Hill with a more complex sound system since the creatures almost never had any kind of footstep sounds. It was pretty spooky as-is.
Goes double for the old Former Building, one of the very first dungeons you end up in. The monsters jumping out from behind the corners isn't the worst of it. You also get to meet ManEatingPlants, cave trees that run away if you touch them, moving roots dangling in your face that you need to pass under, corridors with pulsating walls, and giant insects that love to come REALLY close and make annoying sounds that can make you jump when you least expect it. Sweet dreams.
Special Effect Failure: Some scripted events will use special animations (like characters trowing objects or firing weapons, or more commonly, explosions) which are actually animated screens, imposed over the main window. They cover up interface objects like the clock or the monster eye, and are not always aligned with the background. In the above mentioned cutscene with the fireball, Tom's entire front may disappear until the impact.
Many 2d sprites are way too obvious, especially in the 3d areas. It's possible to look at some Iskai buildings from an angle that exposes the enormous roof cupolas's (2d sprite, always paralel with the screen) "corner" sticks out behind the wall (vertical plane fixed in a 3d space)
The storm demons are far worse at not looking like cardboard cutouts than most creatures. Also, they are the only demons that leave behind a corpse, even though it's not logical, being giant floating clouds with vague humanoid figures in them. Said corpse looks like their sprite was slightly twisted using photoshop, and remains stuck in midair, obscuring much of the battlefield. If you try to move any closer, good luck at seeing anything other than a big gray circular canvas with a bad Munch imitation drawn over it.
That One Level - The Khamulon. It is extremely long and full of repetitive encounters combined with empty rooms. It nearly drove the author of the aforementioned Let's Play mad.
Other players find that one of the best dungeons for its length, sense of danger (you cannot just escape from it and return later), complexity and some ingenious traps, and would rather point their finger at the caves - the engine is really bad at rendering "natural" dungeons and navigating them is very frustrating.
Uncanny Valley - intentionally invoked with NED. Most character portraits show a friendly smile or an aloof no-nonsense attitude and will allways show at least some personality. NED's expression is completely blank, as if he's looking right through you.
Viewer Gender Confusion - Drirr has been mistaken as female occasionally. Given that he's an anthropomorphic cat-thing, though...
The Woobie - Poor Bradir. His best friend blackmails him into killing him, then leaves the guy to deal with the whole ordeal all by himself. Dick move Akiir.