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.
Anticlimax Boss: Bonechill, the Chapter 7 boss. He's the leader of the Skellobit invasion, implied to be the Mario equivalent of Satan, and personally attacked Grambi... but is a serious pushover. Sure, you can only hurt his head, and Thoreau and Luigi can only attack the head... however, get them both out, then have Luigi super jump. You'll deal double damage from the jump, but what really does it is how you can repeatedly bounce on his head. If you don't kill him the first jump, if you can use Thoreau, do it, then super jump. Let's get a little more specific: Bonechill has 80 HP. If one is to kill most of the enemies you can and got the Power Plus, you should have around 8-10 attack. And super jumping deals double damage... yeah... Bonechill becomes the easiest boss in the game, and he's a late game boss who was designed to make a great emotional impact. It's even worse if you played the previous two games before this, as the Crystal King and Magnus von Grapple 2.0, the other Chapter 7 bosses, were rather challenging bosses.
If you have Luigi when you battle Wracktail, he's easier than Fracktail, since you can just super jump the horn. Otherwise... not so much. And Shadoo can be this if you're at a high enough level when you get to him. And considering what comesbefore him, that's not all that unlikely.
Best Level Ever: Chapter 3, with its pixel-like art design, getting a lot of useful Pixls, and especially Francis and using him to poke fun at Otaku people.
Complete Monster: Dimentio. He's pretty entertaining for most of the game, but by the end, he's just plain freaky. To give you a pretty good idea as to why he qualifies for this trope, he cracks jokes when causing Mario, Luigi, Peach, and Bowser's deaths, and he also plans to stab Count Bleck in the back and gain control over the Chaos Heart in order to ensure that all dimensions but his are destroyed so he could recreate the universe in his image and implies that he intends to torture Bleck and his followers as soon as he's killed Mario. What seals his fate as a Complete Monster is, after being defeated by Mario, Peach, and Bowser, he ends up deciding to erase all universes anyway as he is dying, meaning that his final action was one that would ensure the deaths of what is implied to be at least trillions of people.
It's widely speculated that Mimi is the Queen Pixl, the flawed original attempt at creating a Pixl that turned out evil. And also that she's the result of a witch's experiments to try and create a potion that allows the drinker to shapeshift.
A theory on Dimentio is that he wrote the Dark Prognisticus (which would make him pretty old.) There's also the question as to why Tippi recognizes him the first time she sees him.
He's also possibly the son of the guy who first created the Pixls, with his daughter being the one who, outraged at his treatment of the Pixls, became the Queen Pixl and led the Pixls to war against the Ancients. The son vanished as a result of this debacle. If all of the above is true, that means that Mimi and Dimentio are siblings. Holy crap.
It's also possible that Dimentio is Merloo, one of the four sages in the Tribe of Ancients. Both are described as being powerful, dimension-controlling magicians, and both wrote one of the Prognostici. If Merloo and Dimentio are the same person, this means that Dimentio was a leader of the Tribe of Ancients, and he wrote both the Dark and Light Prognosticus.
Harsher in Hindsight: If you beat Shadoo in the Flopside Pit of 100 Trials, you get a post-battle comment, unique to whichever character you were using. Luigi's line is "Even if he was a fake... I don't ever wanna fight my Bro again!". All well and good if you go through the Pit after completing the game, but, though difficult, it can also be completed before fighting Super Dimentio.
It's implied that Floro Sapiens have no sexual dimorphism. All four paintings of the former rulers look exactly the same except for coloring, the second of which is confirmed as female.
Vindicated by History: This game was met with a Broken Base when it was first released, mainly because not everyone was pleased with its choice to ditch turn-based battles and the reduced difficulty. Nowadays this has mostly died down, especially with the release of Sticker Star, and people who once loathed the game tend to generally view it as different but enjoyable game with a great story, almost like a spinoff of a spinoff series.
What Do You Mean, It's Not Symbolic?: Chapter 7 is full of it, such as the forbidden apple that brings trouble when eaten, the chapter boss being a former Nimbi who was exiled to the Underwhere, the Nimbis' battle with the Skellobits, and the fact that the daughter of a seemingly deistic figure sacrifices herself to save the universe.
In Sammer's Kingdom, you might notice lycoris flowers growing along the path. In legends, they're often believed to grow when people who meet shall never see each other again. Pretty epic foreshadowing for The End of the World as We Know It.