How come Otome's friends get away scot-free? They don't. See Karma Houdini or the WMG for the reason why.
Why there's no bad ending in Cross Days where Roka or Ai kills Yuuki? One is Yuuki's Nice Guy status. Two is how neither girl is as emotionally unstable as Kotonoha or Sekai, especially Ai, who, despite her Mad Love personality, is willing to give up Makoto and Yuuki and let them be happy with who they chose.
Why is it that Setsuna is willing to do anything to ensure Sekai's happiness, even at the cost of her own? It's revealed that Setsuna and Sekai are, in fact, half-sisters, with Shun Hazama being their father, and Mai and Youko being their respective mothers. In School Days, Youko, Sekai's mom, makes it apparent that she hates Shun for not being faithful to her. Shun eventually gets together with Mai instead of Youko. It's possible that Setsuna feels guilty about her parentage, and feels indebted to Sekai.
It's shown that Kotonoha's attractive body is a major liability to her self-esteem, fueling the depraved lusts of the boys who ogle her body and inciting jealousy among the other girls. So why does she start appealing to Makoto's lust to keep his attention? It's quite simple: Makoto was the first person to notice Kotonoha just...for her, not for her body. This allows her to open up to him and form a friendship, confiding in him and ultimately offering her body to him, presumably for solace. It's her first taste of sexual pleasure. She learned that day that sex was a means to stay close to someone. She wasn't just trying to appeal to Makoto's carnal desires. She was trying to stave off her persisting loneliness and self-esteem issues.
Itaru Itou lives with her father, Tomaru. The one who already impregnated several of his underage daughters, sometimes with the aid of fertility drugs. He's also responsible for ensuring that Makoto is either a cousin or an uncle for around half of his potential love interests, including Sekai. At one occasion, when she runs away from home to visit Makoto, she tells him she hates their dad — hopefully, hopefully, this is only because Makoto is so nice to her that her dad is unlikable by contrast.
Don't know if this helps you a little, but according to a possible route of Summer Radish Vacation 2, Tomaru was castrated by Rideru Takatsukasa (basically, rendering him impotent). It's unclear whether or not this development carries over to the School Days canon, however.
