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.
Alas, Poor Villain: After you defeat King Croacus in Chapter 5, the Floro Sapiens will come by and tell Mario and the gang that he wasn't evil at all. He only kidnapped and brainwashed the Cragnons because they were dumping their trash in the river and contaminating the water the Floro Sapiens drank from.Oops.
Complete Monster: Dimentio, who cracks a joke at killing Mario, Peach, and Bowser, and plans to destroy The Multiverse and remake it in his own image.
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.
Family Unfriendly Aesop: Instead of diplomacy, the correct answer to one country poisoning another's water supply is to kidnap and brainwash the people from the former country and force them to serve your king, to be fair, it is implied that the poisoned water drove said king insane... doesn't make it any less family unfriendly, though.
Memetic Badass: The Green Thunder, Mr. L! And no, not Luigi; Mr. L.
Narm: Admittedly, some people might find Bleck professing his love to a technicoloured Pixl butterfly at the end kind of hard to take seriously, even if it is a Paper Mario game.
Tear Jerker: After accomplishing his mission, Squirps, the last of his kind, lays down before the statue of his long-dead mother and quietly slips into unconciousness.
"Phew! Now that Squirps is all relaxed, Squirps feels kinda...tired..." said Squirps. And with that, Squirps lay down before the statue of his beloved mother. "Mother..." he said, his voice soft. "I did my best, right? Are you... proud...of me?" Then...slowly...young Squirps closed his eyes...
No need to open the waterworks. Once you return to Outer Space after you beat the game you'll find Squirps safe and sound. He really did just sleep for a while.
They Changed It, Now It Sucks: It's a very fun platformer, and this game is proof that a Mario platformer can have story as well as good gameplay. However, those who wanted the usual RPG weren't exactly happy with this game.
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.