Super Buu may have more ki and be able to contend with Vegito in a serious 1v1, but the form amounted to nothing because he was too human, thus too complacent.
Kid Buu is a pure menace. The second this form appeared, everything was doomed, not just Earth. There's a reason why the pure malice was a cosmic-level threat, something Super Buu can be, but won't, because he, like Perfect Cell, had lost his thirst for destruction once he learned to appreciate fighting for the sparring alone, not the inflicted terror.
By ki measures alone, Super defeats Kid. But the characters don't act in a vacuum; they have personalities and motivations, and Kid's push him to be a far stronger opponent than Super.