In my opinion, Superman is the most powerful Kryptonian because he's the only one that truly exists. But for the sake of the argument, putting aside this opinion, I would still say he should be the most powerful of the Kryptonians like him. He grew up on Earth with these powers from an early age, so he's very experienced in using them.

And if all of his adventures as Superboy can be in continuity, then that's a lot of experiences--fighting and teaming up with hundreds of other super-beings. At the same time, he's gone through so many experiences where he doesn't have powers or he's a girl or he's an ape or he's blind, that by the time he's a Superman there's almost nothing he hasn't had to endure. And what doesn't kill us makes us stronger.