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.
Also, Risa never apologized to the other girls for her actions in the game.
Author's Saving Throw: Rihoko's story continuation in Amagami SS+ where her and Junichi finally get together has brought a lot more appreciation towards Rihoko's arc nowadays seeing how the fanbase went ballistic knowing Rihoko lost out in her own arc in the first Amagami season.
So far, these scenes are: Junichi getting on all fours like a dog and kissing the back of Haruka's knees, and Junichi going down on Kaoru's navel.
Sae's arc takes a slightly different turn on this and has doctor fish feeding and tickling her feet.
A bit too early to say if it's all what we're going to get for Nanasaki's arc, but Junichi and she get a weird hallucination where she's a bowl of ramen and she's saying how he will "eat [her]", which ends with him kissing her finger. It's short and weird, and later in the park they get a conventional kissing scene. Truth be told, it's a bit disappointing.
While not as... unconventional as the memorable kissing scenes of the first two arcs, the last episode of Nanasaki's arc has them do a naked onsen kiss. Definitely better than the previous episode's offerings.
The second OVA had some nice intimate moments: in Nanasaki's arc, he puts his hands in her skirt pockets and tickles her there, and in Rihoko's arc, we find out that she has very ticklish feet.
Hibiki might also count in a lesser degree. Aside from not being a main character, she has some fans and a healthy amount of fanart. She also has three specific episodes in Various Artist which are quite a lot for a side character for Haruka and Ai.
Fanon Discontinuity: A lot of fans are already raging hard enough to say that Rihoko's arc never happened.
Hilarious in Hindsight: In the bath, Kaoru ponders her new feelings for Junichi and thinks he hasn't changed while she has. But (in the anime, at least) she's wrong, since Junichi has been having at least sexual thoughts about her.
Later, out of the blue Junichi asks Kaoru if she has someone she likes; she refuses to answer and asks him the same question, to which Junichi just replies "no". While this scene illustrates their attitudes at this point of her arc, it's also made funnier/poignant by the foreknowledge that Junichi isn't exactly being honest.
Ho Yay: Junichi gets his fair share with Umehara. Between claiming to share a 'Lover's Parfait' with Umehara on a date with Haruka, and the two of them becoming the protagonists in a Yaoi manga by Sae, one has to wonder. Never mind that in another Haruka event, Haruka competes against a man, who, on the condition of his victory, gets to take Junichi on a date.
Hype Backlash: Lots of fans went into the anime thinking that it would adapt the best route of all the girls (see Adaptation Distillation on the main page). But after getting only one arc adapted faithfully and the others a mish-mash of routes and original content, some even getting CENSORED outright, fans are starting to get irritated.
The Woobie: Kaoru's soft-spoken friend Keiko. She confesses to a guy and waits a month for his answer. Instead, the guy just asks for a kiss. She turns to Kaoru for advice, who then recruits Junichi for a male perspective. Junichi suggests writing a letter requesting a proper reply. Keiko spends a lot of time writing the letter, only to have the guy and his cronies pass it around and laugh at it the next day. Kaoru does not take this well. To be fair, said guy and friends get a calm but stern reprimand from Tsukasa, and they're shown reflecting on their actions.