Perhaps the biggest problem in the whole show to me, is that everything rides on the main character being some amazing genius that everybody wants.
However, I didn't feel like we ever saw this at all. We were just told "Oh, he's supposed to be super amazing", and we only ever see him fumbling around with politics like an idiot.

The whole plot line of Iris being Nagisa seemed to be completely irrelevant.
The cartoon cutout villain of an older brother was just too silly.

Even the romance scenes seemed far out of left field. Main guy's little sister talked to him a couple times and helped him with his homework. And now suddenly she's in love with him? What?

The arguments the CEO makes are just dumb. "We can't revisit our decision. Don't you know how companies work?"
Lol, what? That's the whole reason for not considering reinstating A-TEC? He could have easily gone with the flow, kept Kaito, kept A-TEC, and then he'd have his "amazing" engineer, who would never work on the weapons project he wanted anyways.

I just couldn't get behind any of the plot elements in this show.