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.
Designated Villain: Meade and Deanu are never shown doing anything evil, really. Meade just plays music for his monsters, who appear to like it (though he does say that he uses it to brainwash Krubble), and Deanu seems extremely ambivalent to everything and is content to just play with Aquid and swim all day. It's unknown if he even interacts with the monsters on his beach at all.
Esoteric Happy Ending: Chomp unites with his mother and Ellie gets to go home! Except... The two friends split up and might not see each other again. The kid kings are good now, but remain in the Monster World instead of returning to families that presumably miss them. And while Priscilla has been dethroned, she remains in the world where she still has a small measure of political power...
Game Breaker: Raising Chomp's Paladin form to get the Healing skill makes the game infinitely easier. Because it's very easy to restore Chomp's stamina, it's basically free (though slow) healing, and can be used to heal yourself up completely at every safe spot.
Drill Em Mister probably counts as well with the amount of Combos it can get off.
Guide Dang It: The effectiveness of items unlocking new forms decreases as the adjacent forms increase in level. Nowhere does the game tell you this. This can potentially lead to some forms being Lost Forever, or at least taking extremely large amounts of time and diligence to unlock.
Scrappy Mechanic: For almost the entirety of the game, the powerups you need next are on opposite sides of the entire game world. This means that you will frequently be travelling across areas you've already been through much more often than you will be actually exploring new areas. This tedium could have been avoided with portals or Doors To Before like most other Metroidvanias have, but, unfortunately, this game doesn't have them.
That One Boss: Zoe and Mister Lobster. The difficulty is much greater than that of the previous boss, as there's a lot going on at once after you've inflicted 50% damage, and the disfigured bunny has a rolling attack that gives you barely any time to dodge. Chomp is certain to go down a few times, not to mention Ellie.
It's Short, so It Sucks : Generally the biggest downside is thought to be the games length. Though going for 100% completion makes the game longer.