I think it's pretty clear - idiots make good drama. Smart people know how to solve these situations better.
Also, you have to understand that the harem genre is a fanservice one. The target audience it's aimed at enjoys girls throwing themselves at the main character even if he's worthless.
There's a few exceptions in the harem genre, but in general this stuff happens a lot. More often than not, they don't do justice to the corresponding visual novels...can't speak for School Days because I haven't played it though, but it seems that people are happy enough with the conversion as Makoto was widely hated well before the anime either way.
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