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.
Big Lipped Alligator Moment: The entire Astarica sequence. Some unknown voice commands Ark to drink from a goblet, which sends him into a fever dream featuring expies of various allies, culminating in a scene where Overworld Elle acts out-of-character and kills two people before mocking Ark who apparently dies from drinking out of a goblet. Nothing within the game hints at any of this, it doesn't affect the plot and never comes up ever again. Ark even comments to this effect afterwards.
Complete Monster: King Henry. He raided a village and killed all of its inhabitants for treasure...except for a young girl he orphaned himself, who he only keeps around to wait for her to spit out the secret of the treasure. He's also described as an extremely oppressive tyrant by the townspeople.
Crowning Music of Awesome: Most of the soundtrack. Remarkable in that the game's composers, Masanori Hikichi and Miyoko Kobayashi, are obscure even by video game music standards.
Genius Bonus: The resurrection of life on Earth follows the order shown in the Book of Genesis.
Also, Crysta wasn't an original creation of Dark Gaia, it was merely a copy of Storkholm. This fits with the Biblical saying that Satan cannot create original life.
Germans Love David Hasselhoff: This game is often nicknamed as "The European Chrono Trigger". As in a JRPG that got some people of the other side of the Atlantic pretty jealous because it was not released there. Although the game wasn't financially successful, it got a very devoted cult following.
That One Boss: Bloody Mary. She has higher HP than any of the bosses before her, while coupling it with insane defense. Her attacks are also incredibly powerful. Fortunately (perhaps as an act of mercy), she's the only boss you can use magic on.
The Woobie: Ark in the ending, and earlier when he realizes what his purpose is.