Getting all of the Stars of Destiny in Suikoden III results not in the typical alternate ending but only in a scenario in which you get to see events from the antagonists' point of view. This isn't just to be annoying: the last four Stars are the antagonists themselves, who never actually join the main characters. —Cat In Cyberspace
The reason why in the end of I, Soul Eater rejects Windy, it is not because simple Even Evil Has Standards. But more like how Soul Eater feeds, it fed on the souls of those close to the bearer. On the other hand, Windy has never accepted anyone in her heart, constantly only thinking of herself and her desire to destroy the world for self-revenge, she doesn't even open her heart to Barbarossa. Therefore, Soul Eater refuses to be hosted by Windy because it'll end up hungry with no 'close friend's soul' to consume.
In the first game, you help capture some mountain bandits - Varkas and Sydonia - by order of the Imperial Army, for whom you're working at the beginning. Later on, stuff happens and you become fugitives from the Scarlet Moon Empire, and join the Liberation Army, who asks you to return to the bandits and free them (as they were strung up and left to starve to death in the hot sun). After fighting your way through the mayor's mansion, you free the head bandit, Varkas... but when you go to free Sydonia, he just teleports out of his own accord. And when Varkas asks him why he didn't do that sooner, Sydonia simply replies that he couldn't very well escape without Varkas. It's meant to be touching and show that despite his aloof demeanor, Sydonia really cares for his boss... but why the hell couldn't he just teleport himself out and then untie Varkas? It's never addressed or even hinted at.
In recruiting Oulan in II, you have to make an all-women party and then get accosted by ruffians that knock you down and they attempt to kidnap the women. This can occur anytime after you get your HQ. The question is, is there any reasons other than Gameplay and Story Segregation that these guys can overpower a party of ladies that have defeated frickin' Luca Blight? Forget Georg Prime, these ruffians are the true Memetic Badass of the Suikoden universe...