Except Junpei really isn't like that. His progression is gradual, and in the female path, he gets over "but our leader is a girl thing?" pretty quickly. From what I recall, he had an alcoholic father or something, and his character evolution has much more to do with him just processing everything that happens around him, with Chidori being only part of his whole character arc. Even before he meets her, he comes to accept his role in the group as not the leader earlier, even if he doesn't fully embrace it until later. It's kind of unfair to describe someone dealing with such a crippling inferiority complex (that he deals with on his own, no less) as an irredeemably bad person who deserves to be cut from your life.

I think we just have different approaches to what we expect from characters in games. I like my characters to be flawed. I like it when a game is frank about human nature because irl it's a very unhealthy thing to expect that people you want to be friends with will be perfect people who will just love you unconditionally and will never have any friction with you. I want a game to show me that you can be amazing friends with flawed people, rather than giving me a completely unrealistic scenario with perfect friends that will ultimately make me only depressed because friends like that can't exist in real life.