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.
Even Better Sequel: Blue World addresses several complaints about the first Endless Ocean and sacrifices very little in the process.
Nightmare Fuel: The Final Boss of Blue World, two Goblin Sharks and the Okeanides Guardian. Dear god the Guardian. It's even implied in-game that the Okeanides people selectively bred it to be scary! (though how they got the phenotype to stay dominant in the goblin shark population without intervention for thousands of years is a mystery).
Tear Jerker: Kat's backstory, and the secret cutscene unlocked by sitting on the deckchair at sunset.
And then, in Blue World... Jean-Eric's son (and Oceana's father) Matthias became trapped in his submersible 650 feet down in the Zahhab Depths while researching the Song of Dragons; he died attempting to escape and left a message for his father in a waterproof case explaining why his work was important to him and that he loved his family very much, giving his old man something to shoot for once more.
Sidequests heavily imply that Matthias is still alive but the plot thread is never fully resolved.
That One Boss: Thanatos shows up once in the main storyline and a few times in other quests. He's immune to the pulsar gun and needs to be avoided or fled. No so easy when you have to search his area for a salvageable.
Even worse on one particular side quest, where you have to distract Thanatos and keep him away from another diver. Unless you're good at dodging, you're going to lose a lot of air.
That One Level: Ciceros Strait. It's swarming with sharks and whirlpools. The whirlpools block off a section of the map during the day, so you have to go there at night - and put yourself at risk of running into Great White Sharks or Thanatos, who tend to lurk around wrecks with salvageables around them.
That One Side Quest: In Blue World, making one million dollars to excavate the Okeanos temple after you complete the main story. Most jobs you take that even reward money and not equipment pay a couple thousand at best, so you have to spend several tedious hours do some same jobs over and over again. There's no hint of this quest coming up, so if you've been spending all the money you've earned so far on other things you're screwed.
The game then pulls a rather annoying fast one on you: turns out you can reopen the temple for half that, but the option still isn't available until you've gotten the full $1 million. The result being that you can then purchase pretty much all the best equipment and the items for Nine-Ball Island at once after the temple's been opened, which is nice, but many players will probably still feel annoyed about the Fake Longevity.
Ugly Cute: Lots of the fish are pretty in really bizarre ways.
Even an In-Universe example, as Oceana squeals over many of them.