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.
Les Yay: Ichika & Manatsu. It's rather subtle, until Manatsu kisses Ichika. In the manga, Michiru obviously has a thing for Ichika. Keiko and Satsuki get their moments as well, which even survives them quarreling over the same guy.
Moral Event Horizon: Saya crossed it before with her "test" and Sadistic Choice, and does it again by putting Ichika in the same situation. She countiously crosses it by punishing anybody that tries to interfere with the test.