I agree, he was really more selfish than manipulative. It also didn't help much that almost all of the girls were pants on head retarded and therefore were unable to resist his aura of smooth.
That said, I genuinely liked this show. Makoto, for all of his selfishness, was fun to hate. Also, I think there should be more harem shows that are more realistic. Not that I'm calling School Days realistic in any sense of the term, but it was definitely a step in a more realistic direction.