Game-Breaker: Hasten Time andO-Overdrive! The ultimate Hydrology spells, both achieved by Spell Synthesis (which can only be performed by Rosalian Mages and Imperial Scholars). Both allow you to instantly end the turn — for your enemies. Overdrive lets the caster then act five times, while Hasten Time lets the whole party get a move in.
Another potential punch doesn't need a cutscene: "Alright, I'll just pop into Weston real quick and WHAT THE HELL IS THAT THING?!" Note that this one can happen even if the player isn't aware of the Jewel Beast beforehand, making it an even worse shock for unwary players.
That One Level: The Isle of Evil. Features folding and moving stairs that accelerate the higher you climb; the slightest misstep sends you right to the bottom of the tower, forcing you to climb up again. Getting the timing right is... difficult. Oh, and if you leave, that's it: you can't come back. So you have to get everything done in a single trip.
That One Sidequest: In terms of getting the materials for it, Gray upgrading his Falcata is no easy feat, especially the specific type of Mullock needed to complete the quest, you just need to spam Blunt Strike many times in battle (Blunt Strike does no damage and may paralyze the enemy)