It is the Supreme Intelligence, you're right. Yon-Rogg was just a sort of central bad guy while the Intelligence was like the overarching bad guy

Don’t forget Ronan the Accuser.

He was more of a minor villain

It would be the Supreme Intelligence

Yon-Rogg, Ronan, Korath, Minn-Erva and the others are secondary/minor antagonists

Exactly, bro

Sorry, thought this was for the Sequel. My bad

Supreme Intelligence was the overarching antagonist while Yon Rogg was the main antagonist

"That's what I said!"-Nick Fury

I hope for see the supreme intelligence form of comics in the futur

It's kind of like Hawkeye, where Kingpin was the real big bad of the show with the Tracksuit Maffia being the side villain, made the big villain in marketing...