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.
Big Lipped Alligator Moment: The sex scenes in the original game suffer from this. They happen and then they're never mentioned again (beyond the screen immediately afterwards), even if the follow-up scene would warrant a mention. Particularly glaring in Shiori's and Ayu's scenarios, where one of the characters reminisces about everything they've done together and mentions everything except the sex. Makes it kind of easy to make the clean version, huh?
Ensemble Darkhorse: Akiko Minase is quite popular with Western fans, to the point that some are surprised that she doesn't have her own route in the game. For proof, see the sheer amount of fan art starring her here: 1
Sayuri, too — she outperformed the entire cast by a wide margin during Saimoe.
Some people are surprised that there aren't more Yuichi/Akiko shippers out there. In fact, they also found it surprising that Akiko doesn't have her own story path in the game.
The doujinshi series Akiko-san to Issho tries to fix this, at least in fandom.
Kaori also has a lot of fans who wish she'd had her own route. Key giving Kanata her own route in Little Busters!Ecstasy may be their form of apology.
Sayuri/Mai. Even Yuuichi ships it at one point.
"Funny Aneurysm" Moment: The first episode establishes Yuuichi's gadfly/troll nature by pretending to have forgotten Nayuki's name and teasing her, in response to her question of whether he remembered it after seven years of separation. We also had Nayuki's "Liar..." played for domestic comedy later in the same episode. Then Episode 22 comes, and we find out Nayuki's side of the scene: she was truly afraid that Yuuichi had forgotten her after seven years, and was dead serious when she asked him whether he remembered her name. In addition, her "Liar...", said in the midst of a Heroic BSOD, punches harder than before. Ouch.
On a smaller scale, there's Makoto's Verbal Tic, "auuu". It turns from cute to tragic once it becomes the only thing she can say.
Germans Love David Hasselhoff: While Kanon '06 is rather popular and beloved in the West, in Japan it seems to be all but forgotten entirely, seeing how it always performs like utter crap in popularity polls while its "siblings," Air and CLANNAD, do much better. Especially Clannad, which almost always wins "biggest Tear Jerker" and similar awards, something quite egregious considering how much it owes to Kanon in the first place, so you'd expect people who likes one to like the other and vice versa. Then again, it was the second TV anime for a (at the time) seven year old, repeatedly rereleased PC game; there may not have been much left in that well.
Also see their results on the original Saimoe: Air got one girl in the Top 8 and Clannad got 3 girls in the Top 8. As for Kanon? Sayuri managed to make the Top 16 (Round 4) but that's it. And not one of the other girls on the show even made it out of Round 2.
I Am Not Shazam: Ayu's name is not Kanon. The main character of that otherseries called Kanon linked at the top of the main page is named Kanon, but Ayu is not.
Les Yay: Mai and Sayuri. They are very, very close, to the point that even Yuuichi briefly wonders in the VN about them. Probably reaches a high point when Sayuri remembers with great fondness how for her last birthday Mai bought her a ginormous bouquet of flowers. And then there's the Threesome Subtext...
Mis-blamed: Mai's aunt was the one who made her display her powers on the television show (and they wouldn't let her leave until they did), not her mother.
Actually, nothing was ever said about her aunt, nor was it stated that Mai was actually forced to exhibit her powers. For all we know from the flashbacks, she might have simply gone along with it without knowing what would have happened afterwards.
Questionable Consent: Some of the visual novel's sex scenes are...rather dubiously consensual. First we have Makoto's - the girl barely looks old enough to understand what she's doing even normally, and the fact that she's already beginning to lose her humanity and intelligence and that she seems more confused than anything else during it only makes it worse. And then there's Ayu's - from the beginning Yuuichi says he doesn't really care if she doesn't want to, and apart from a brief moment where she removes her shirt, through the entire scene all she does is look awkward and uncomfortable and tell Yuuichi to stop or that it hurts, which Yuuichi responds to by irritably thinking that she's ruining the mood.
Squick: It's bad enough that Yuichi has sex with Makoto after she begins losing her humanity (or even at all), but they also do itdoggie-style.
Uncanny Valley: Key hatedom loves to point out the characters' giant eyes and tiny mouths as disgusting or unnatural, though it's intended to be cute and much of the fandom sees it as such.