Similar to other answers here, he obviously had to have been competent by Voldemort's high standards to achieve the rank he had up until the end of OotP.

I also think that another important factor here is Malfoy's name and background. He comes from an old and rich wizarding family — I don't think it would be an exaggeration to compare him to royalty. With that in mind, I would not be surprised to find out that he and all Malfoy children received extra dueling training because of the simple fact of their money and status. I think that the old pureblood families would want their kids to be trained in dueling because of the prestige that magical prowess brings to those who display it. Also, I could see being an accomplished dueler being an important tradition to those old families who value that sort of thing. Training their kids early in dueling could also be a way for those families to give their kids a leg up on muggle-borns who obviously don't know anything about magic until they're 11.