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.
YMMV: With Big Shells and Wings
Ass Pull: Peach getting "raped" in chapter 18. It isn't until sixteen chapters later that we find out that a random koopatrol used her Sneaky Parasol and disguised himself as her while she hid under the bed. Twink flat-out lampshades this trope.
Chapters 35 and 36. Mario and his friends enter a series of vortexes that transport them to various stages and mini-games that the Mario Bros. have been to in previous adventures. Um, okay then.
F.L.U.D.D.'s random appearance in chapter 24. Not only is it not explained, but as soon as the chapter ends, F.L.U.D.D. is never mentioned again.
Complete Monster: Dracolin, a sadistic dragon who enjoys burning, torturing, devouring, and tormenting others just because it's fun. Plus he likes grossing out others with childish scatological humor. What's mostly disturbing about Dracolin is that he takes pleasure in scaring little Yoshi children, almost to a point where he comes across as a pedophile. He even crushes one of them to death and then brags to the dead Yoshi's friends how wonderful it felt killing her. To top all that off, it's implied more than once that Dracolin has a Fetish for crushing small creatures.
It Gets Better: The story starts out as a comical fanfic suited for young teenagers. But the further along it goes, the darker it becomes and the more serious the plot is. Some of the tasteless jokes also begin to go away as the story progresses, and many characters start to go through seriously needed Character Development. By the time chapter 37 comes around, the story arguably starts Growing the Beard.