Consider this: If one were to study Maimonidean or Vilnian halacha, he would come to see how each and every ruling fits with the Talmud. However, if one were to study, for example, the Rema’s glosses to the Shulhan Aruch, it would be an exercise in determining and explaining why individual rulings veer from those that seemingly emerge from the Talmud. Therefore, if one were seeking to approach any matter of practical halacha from a critical point of view, that is study halacha as a form of interpretation of the Talmud, he would do best to follow the Vilna Gaon’s methods. The result is usually an intellectually satisfying and honest understanding of the halacha.
From Avraham Ben Yehuda, here.