Here is the full list of all 16 Ys VI: The Ark of Napishtim achievements. It takes around 15-20 hours to unlock all of the achievements on Windows.
Win the duel with Geis.
Obtain every other achievement.
Win a boss fight with 1 HP remaining.
Complete Boss Rush mode on any difficulty.
Complete the game on Nightmare difficulty.
Complete the game in Catastrophe Mode.
Destroy the Ark’s Central Shaft.
Defeat Ernst.
Defeat Majuunun.
Acquire all equipment.
Win a boss fight without taking a single hit.
Acquire every Tabulas.
Defeat Orjugan.
Defeat Ud-Meiyu.
Defeat Zonplas.
Defeat the Wandering Calamity.