It's pretty much been spoiled already, but here's the condensed version:
1)
Makoto was given every language except for Hyuman, because by being one language short, he avoids the penalty of obtaining a godlike power, which would normally kill him. Thus, the goddess has technically blessed him in a way that prevents him from easily interacting with (and her biggest fear of breeding with) Hyumans. Makoto's struggle to speak it is his own self preservation. He actually does learn it, after getting even more OP, and in doing so, it nearly kills him.
2)
Yes, the goddess, over millenia, rewarded and blessed beautiful people to the point she selectively bred the entire Hyuman population—who did used to be human—into physically beautiful but surprisingly weak supermodels. Makoto is ugly by comparison, not ugly by our world's standard.
3) Uh, this one actually will kind of ruin some people's enjoyment if they read this spoiler, so please really do consider not reading this one unless you truly don't care about spoilers that you won't see for another 3-5 years in the manga.
Makoto is legitimately level 1. He has legitimately not earned enough experience to get level 2. The level system accurately levels people according to their species. Make of that what you will.
