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.
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.