- Anti-Climax Boss: Some bosses in the Ark of Napishtim are disappointing compared to others; justified because it's still possible to save the game despite a Point of No Return.
- The second form of "Galba-Roa" is a joke compared to its first: all it does is hit its tail to the ground, creating an obvious Shockwave Stomp, which players can easily avoid by jumping. Sure, it can still take a swipe at Adol by using its claws, but only if players stay in front it for too long while they Attack Its Weak Point; all this is mitigated by the fact the Galba-Roa has slow wind-up speed for its melee strikes.
- Even on "Nightmare Mode", the Final Boss is underwhelming: its first form relies on a Laser Hallway scheme with no direct attacks (aside from flame-throwing turrets, but these can be avoided and/or destroyed), while its follow-up transformation suffers from predictable attack patternsnote and Attack Drones shooting slow projectiles.
- Awesome Music: Please see here.
- Demonic Spiders
- A literal example with spiders after fighting the first boss in the game: this is a point where these creatures deal intense damage early into a play-through via swarm tactics, Stunlocking players indefinitely. The only way to kill them easily is to perform a drop attack; unfortunately, doing so merely leaves Adol open to getting stunlocked from ones the drop attack missed. Later on, bigger versions of these same creatures appear.
- Higher level versions of the "wild boar"-type enemies attack in packs, each delivering high damage by ramming with Knockback capabilities, all the while inflicting Interface Screw Standard Status Effects. Oh, and the Setos, the birds in the Woods of Quatera, have a small chance of bringing in a higher level boar rather than the weakest variant, well before the player is ready for them.
- Game-Breaker: XSEED Games's Catastrophe mode allows the purchase of STR and DEF boosting seeds, which don't have increased costs on Nightmare like with Vitality Seeds. Combined with the Nirva nest in Limewater Cave, it's possible to farm gold quickly enough that farming seeds becomes more efficient than normal leveling. With enough Stat Grinding, it's possible to give Adol high enough stats to brute-force any endgame boss, including Majunun.
- Goddamned Bats: The near-literal bats (Invincible Minor Minions until players find the "Bell of Silence" accessory) in the "Limewater Cave", alongside "Adol clones", which are really tough unless players also acquired the "Rainbow Fragment" accessory to reveal their true forms, making them easier to take down. In fact, the area's boss "Orjugan" even summons the bats at higher difficulties. Furthermore, the scorpions in the underground areas (some of which are invincible on Nightmare Mode), and the dragonflies in the Ruins which shoot in a circular pattern, can easily knock players off the narrow platforms. Finally, color-coded enemies at higher difficulties require players to use the right-colored Emelas Sword on them.
- Polished Port:
- Zigzagged with Konami and its PlayStation 2 port - although they replaced the sprites in the PC version with full 3D models, made it fully voiced and added "Alma's Trials", blood effects were removed to get a lower rating from various video game rating and censorship bureaus. This version also runs at 30 frames-per-second, making it somewhat of a mixed bag.
- Played Straight with XSEED Games's PC port, which runs at 60 FPS, allows Alma's Wing to teleport between most Spirit Monuments, and has Catastrophe mode. It also supports high resolutions and has multiple levels of anti-aliasing, while having low system requirements.
- Porting Disaster: The PlayStation Portable version is generally considered the worst version of Ys VI due to smaller screen resolution, lack of the PlayStation 2 version's extras (such as voice acting) and for having Loads and Loads of Loading.
- Scrappy Mechanic: The "Dash Jump" mechanic can be incredibly tedious to pull off, especially at the Ruins, as players must press the attack and jump buttons simultaneously in order for it to occur, as certain treasure chests in the Ruins can only be reached by using Dash Jump. The PlayStation 2 port of Ys VI, featuring Alma's Trials, requires a player's mastery of Dash Jump to even think of completing it.
- That One Achievement: "Because It's There" in the Steam version, which requires beating a Bonus Boss that can only be damaged if Adol's at least level 50, have upgraded each Emelas Sword to its max and are equipping multiple stat-enhancing accessories. Having a serious chance of winning requires reaching even higher levels, which is extremely frustrating when level 50 is around the point where the game's Anti-Grinding features start making Backtracking through the final dungeon show Diminishing Returns for Balance. Finally, there's no real reward for beating this boss beyond the achievement, as the chest it guards can be claimed as soon as the boss is found (half-way into a play-through) by the simple expedient of merely running around the boss, opening the chest, then running away (since the boss' attacks can guarantee a One-Hit KO). Catastrophe mode somewhat mitigates the Anti-Grinding by allowing the player to farm stat boosting seeds, but it's still a pretty slow process and there's still a lot of Early Game Hell to plow through first.
YMMV / Ys VI: The Ark of Napishtim