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.
Breather Level: Compared to earlier areas of the game, The Veil is absurdly spacious and almost completely lacking in dangerous creatures. Also a literal Breather Level, since you take your first breath of air above the Veil.
To say nothing of the Ice Cave and Frozen Veil, which do not contain a single enemy between the two of them which actively attacks you (and many enemies there can't even do collision damage). They do lead up to a tricky Bonus Boss, though actually reaching it involves difficult moves.
Demonic Spiders: Mutants (mutated Mithalans) in the Cathedral and clockwork crabs in the otherwise relatively sedate Sun Temple—the crabs far outstripping the mutants in terms of trope qualifications. Then there are the things you find in the Sunken City.... Averted by the spider-crabs you see in the Abyss: those are just mobile traffic hazards that run from light.
Giant Space Flea from Nowhere: Averted. The Sun Worm could be taken for this, as it's neither the god that used to be worshiped there, nor a king-size version of the local wildlife, and it's not the personification of the sun by any means. However, reviewing the backstory text (and the art splash screen which you get after defeating each plot-relevant boss) suggests that this is a remnant of the Lemurians, who were transformed into such creatures by their creator when they turned to sun-worship and technology.
Goddamned Bats: Moneyes, though they do have useful drops, being the primary source of two important ingredients for healing items.
Mithalas Cathedral, home of creepy music, disgusting blood vessels and tumors on the walls, giant tumors to fight, and more tentacles than you can shake a stick at.
The disasters which befell the various races whose former homes you're exploring... The ones who were just slaughtered by the Creator got off easy.
The Abyss. Deep, dark water with horrible things lurking in it. You can illuminate the area with Sun Form... which is defenseless. There's even a Blue Whale down there, which is harmless, but still terrifying when it looms up out of the murk. Even Naija gasps in fright when she sees the whale, which she normally does only to announce bosses.
Going through The Sunken City can give you a few chills.
The last boss. All five forms are a different kind of nightmarish. The first is a giant alabaster figure sitting on a throne with a voice that fluctuates between deep and childlike. The second form involves the giant's face popping off, revealing a black void that absorbs your partner, while the legs break off to be replaced by horrible tentacles. The third form is a horrible crablike creature with clutching arms, giant snapping pinchers, and a single staring eye (and did I mention his body is also roughly infant-shaped?). This form stalks you (and vice versa) through a pitch-black maze. After you beat this form, he turns into a freakish spindly babylike creature. The fifth and final form is the most nightmarish of all: A misshapen behemoth with a protruding eye (which you rip out with telekinesis), a huge toothy mouth in his chest cavity (which opens to reveal an infant), and a scream that will haunt your dreams.
Romantic Plot Tumor: Li, again. Totally derails the plot and Naija's motivations — as the RPT page notes, the player basically has to drag her from there to the point where he gets kidnapped. Worse, it affects play: Any time Naija is stationary in Song ("human") form for more than a few seconds, and he's nearby, they'll drift together and start snuggling, regardless of nearby enemies or other hazards. When this happens, he stops shooting, and Naija can't do anything else until you right-click to separate them.
Scrappy Level: The Frozen Veil and to a lesser extent The Veil as well, due to the fact that you have to go onto land at a few points. Unfortunately, you're a sea creature who can't actually walk, only leap around. The Frozen Veil also involves a lot of bubble jumping, some of which are extremely tiny. Exiting a bubble causes Naija to vault in that direction at very high speeds, making it hard to control, and if you fall, you have to start the whole sequence all over again. AGH. On the other hand, both are good places to collect various resources.
No Escape: You have to find an enemy that you would normally never seen on-screen; you have to use the 'look' function to find out where it is and blast it while it's off-screen. Trying to figure out where this enemy is more a challenge than actually beating it.
Super Chef: Finding all of the recipes involves much Trial-and-Error Gameplay, since a good portion of them aren't given out by the game itself, or are dropped infrequently by rare enemies.
Speed Racer: Finishing the Arnassi race in under a minute requires sharp turns, speed-boosting items, and an optional form or two, and even then, it's still extremely easy to get stuck during the circuit, when the time limit is extremely tight as it is.
That One Boss: Octomun. Hope you stocked up on healing foods — you're juggling at least two forms, dodging energy balls and ink-squrting squid, keeping the lights on, and trying to hit a briefly-visible target without getting grabbed and pounded against the floor.