Remember how /a/ used to obsess about Jun, even though the show he was from completely sucked? He was just a meme made popular by /a/, that stuck around far longer than necessary.
Makoto is just like that. School days sucked. From beginning, middle, to end. The writing was bad, and the characters were hideous for a harem show. But /a/ has turned Makoto into a meme. The only thing to do is just ignore it till it fades.