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.
God-Mode Sue: Kyon, in a good way. And Yuki. It's...difficult to explain if you haven't read the fic. Still, suffice it to say the power levels of everyone in this fic are far above those ofcanon. By the time the Resolution arc begins, the combined efforts of the protagonists can solve any problem short of an apocalypse.
In Chapter 1 Kyon tells Ryoko that she is the most reasonable person to ever try to kill him but that he remembers that time she stabbed him all too well. This becomes hilarious later on when we learn another two of his classmates tried to kill him during separate occasions, and when he's fighting for his life against some Yakuza.
This conversation from Chapter 12 becomes suddenly funnier when you realize Tsuruya's line is proven right when Kyon gets two girlfriends, courtesy of Haruhi.
Masao: (To Kyon) But you look a capable sort. Ambitious, too. It takes a strong man to keep two women, doesn't it?"
Tsuruya: My guy is totally cool enough to handle, like, way more than that, you know.
Yuki and Mikuru, even more so than in the original.
Durandall in general doesn't shy away from Haruhi's bisexuality; she gets flustered when she is offered a chance to get better at kissing from Yuki, and even more so when Kanae calls her sempai for the first time.
Tsuruya and Mikuru, too, although it could be argued that's more Like Sisters.
"...but I digress. When you get that feeling, you know the one, in the back of your head? The one that makes you think something is off about the situation? It may be right. Granted, you may also be tumbling headlong into a fit of paranoia that will end terribly for you and everyone you love. ..."