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.
Anti-Climax Boss: Kuyo was built up to be the Big Bad of the enforcers arc but was knocked out by Ranma in one blow. This might be justified because Kuyo really is a very powerful monster but went up against the wrong opponent. Ranma's Hiryu Shoten Ha is a technique that relies on an opponent's hot battle aura (or regular heat) and the hotter the aura the more powerful the Hiryu Shoten Ha gets. Excluding Kouma, Kuyo is perhaps the most powerful fire-based monster at the school, so when he attacked Ranma, the blast was huge and more than enough to knock him out. Without Ranma, the heroes probably would have had a lot more difficulty defeating him like in the manga and anime.
Ranma also lampshades how anticlimatic it was to knock out the big boss in one hit. Apparently, he thought that Kuyou was a random Mook and would have dragged it out more if he had known who he was dealing with.
Ensemble Darkhorse: It turns out the Netherworld monsters were only supposed to appear in their introductory chapter to get beaten by the heroes and Richard, but they have since become recurring characters.
Foe Yay: Ranma and Inner Moka just a bit. He acknowledges her as one of his most challenging opponents on the campus and even asks to fight her again so that he learn how to do her insanely powerful kicks. She seems a tad bit focused on beating him and proving her superiority and after their fight apparently talks to Moka about him quite a bit, usually with rather antagonistic messages for Ranma.
"No paraphrasing! Tell him his eyes are mine!"
"Come on, let me out! He's literally asking for it!"
Harsher in Hindsight: Outer and Inner Mokas' arguments can come across as this at times, especially if you read the more recent chapters of the manga. Their relationship is a lot less stable than it is in canon and it can be a bit chilling to read Outer-Moka telling Inner-Moka that with Ranma around, the heroes don't need her to come out to fight, rendering Inner unnecessary. In the first After School chapter Inner-Moka calls Outer a facade and an illusion of a soul created by the seal that does not exist while the rosario is off; Tsukune even lampshades it as disturbing only to be cut off by Kouma to save it for the main story. These issues are very emotional and traumatic to both Mokas in the Fairytale arc.
Hilarious in Hindsight: This story was posted with the first three chapters on September in 2009, a month later we're introduced to Fang-Fang Huang in the manga, an obvious expy of Ranma, what with the braid, chinese clothes (in this case he is chinese), androgyny (in Ranma's case he is either a masculine boy or beautiful girl at a time), panda and later realizing his gift for martial arts. What makes this doubly funny is that that Black Dragon says he hasn't read the second season of the manga when he started writing this fic.
Ho Yay: Ranma and Tsukune's friendndship definately shows signs of this; the fact that Ranma can transform into a beautiful girl just adds fuel to the fire.
Even people in-universe comment on it.
Jerkass Woobie: Saffron is still an uppity, little jerk but you kind of feel sorry for him. Constantly getting killed by assassins (some of whom are his subjects) back home, plus students and teachers at the school, repeatedly eaten by a giant spider, can't access his true power because of the seal, and getting replaced by a heater. Saffron is trying to get on more friendlier terms with Ranma, but because of his own smart mouth, or Ranma being distracted and brushing him off, it ends in failure and makes him more pitiable.
Les Yay: Yukari's crush on Moka obviously. Unlike her admiration for Ranma, her feelings for Moka are 'not' above base lust and sexual attraction. Naturally she tries to spend some quality time with Moka whenever she gets a chance.
"Well I WAS here to talk to you about renewing bonds of friendship and seeking forgiveness and stuff like that," Tsukune began, "but I have to admit that now I'm much more interested in why Yukari is in your room half-naked."
There's also the male students asking if Kana and Mizore were going to make-out after their Cat Fight.
Never Live It Down: Ever since Ranma's fight with Kuyo, students now bring up that he can summon tornadoes at will.
They Wasted a Perfectly Good Plot: Since Goblin is a dead language Tsukune lost a powerful weapon when he accidentally caused the war golem Morticullus to self destruct since no one else but him could control it.
The fact Jedite knows goblin is a dead language could count as well
What the Hell, Hero?: Even Yukari started calling Moka out for her knee-jerk reaction of believing the worse in Ranma.
Yukari: Moka, Ranma is far from the only one who might seek to inflict harm upon me; there's no need to accuse him every time something goes awry.