A bit of a rough mess, Medaka Box reminds me of playing a video game directed by Yoko Taro. It's kind of an insane mess and sometimes is... not very good, but in the same breath has the ability to give the audience something totally unexpected and amazing, that they didn't even know they could have. It's hard to explain without spoiling it, but I can say that for the most part its one hell of a ride. I still feel pretty confused because I want to believe that NisiOisiN was writing pretty intelligently with actual themes in mind (sort of like how Fire Punch went about doing things, for a reference point), but at other times it's like he's not even trying at all.
I feel like NisiOisiN was trying to write a meta commentary on shounen powerleveling anime, but he got lost along the way. I think that with some trimming of the fat and a rewrite to bring everything a bit closer together, this could be a genuine 10/10, but that probably won't happen since this manga wrapped up three years ago.
tl;dr: the highs are very high, but this manga has it's fair share of lows as well.