Makoto is designed explicitly as a blank slate you project yourself onto. I think the reason he comes off as a dick/manipulative is because it was their first time trying S. links so the choices are pretty limited to "agree or "disagree" without any real personality behind them. Also his character design doesn't really help much. I imagine if he was a given a more cheerful look people wouldn't be so negative.
They never really give him a background
so you can guess about his past/personality however you want. I think its more fun to imagine him as being a straight baller at his old high school where he got all the chicks and had the tightest bros. He was probably so disturbed by everyone in SEES' fucked up mental issues that he became a mute.