In short, Hegel benefited from having his ideas more clearly worked out and regularly published which led to followings that became influential within continental philosophy. Hegel's authority has been a hallmark even for the enemies of his thought. And so it has become acceptable to ignore Schelling, but not Hegel. But as our historical reflective distance expands it is more evident that we cannot ignore either, especially the former.
I take you to be inquiring into the dominant grand narratives of Western philosophy which take Hegel as a leading figure while Schelling is just lumped in with Fichte as the triad of German Idealism. Professional and popular culture philosophers alike have perpetuated this account. The beef between Schelling and Hegel is well-documented and given Hegel’s rising stature in taking over Berlin, many find Schelling’s later works as personal attacks of jealously. Schelling’s last public lectures on mythology and revelation are deemed largely as theosophy or “spiritual channeling” offering only religious or theological value. The conventional wisdom is impoverished and ignores Schelling’s own contributions in attempting to breakout of Hegel’s spell of logocentrism. There are several important differences between Schelling and Hegel that have been underappreciated. Given their connections, such as, being roommates in 1795 or editing a journal together, etc. a more serious problem persists involving the conflation of Schelling and Hegel. Zizek's reliance on Hegel's logic as the basis for his parallax ontology relies on a smuggled in reading of Schelling's later philosophy is a typical example of such misconstruing. Presupposed in his interpretation of Schelling's second draft of the Weltalter is the consistency between Schelling's attempts to overcome German Idealism with the mature Hegel's logic as the completion of the Idea for the transformation of positing substance as subject. You will not find this philosophical approach fruitful regardless of Zizek's aims at perversity and sleight-of-hand. Reading Schelling's philosophical journey as providing the ground for a materialist ontology or Marxist-oriented social critique is irresponsible rendering, in my estimation. This also involves the trouble with associating Schelling’s thought with the psychoanalysis of Freud or Lacan. Clearly, Schelling is credited as the first to develop a notion of unconsciousness in his philosophy but he dealt with it on a cosmically experiential level and not as some faculty human beings carry around in their heads.
I applaud efforts at showing Schelling’s relevance to our world despite taking some of these approaches to be misleading. A Schellingian renaissance of sorts is taking place while much of Hegel’s authority has been challenged or eclipsed. Schelling moves us in the direction of contemporary philosophical sentiments which are pluralistic and, unlike Hegel, opposed to rooting history in Absolute Spirit with its apex in modern Christian Europe, but rather in a meta-drama of the fusion of “world-consciousness.” I see his thought as a springboard for American pragmatism and process philosophy and this is evident in the volume edited by Catherine Keller and Anne Daniell, entitled, Process and Difference: Between Cosmological and Poststructuralist Postmodernisms (2002). As Jerry Day notes in his book, Voegelin, Schelling, and the Philosophy of Historical Existence, (Columbia: University of Missouri Press, 2003, p. 143) “Schelling does not take the self-consciousness attained at the end of his reflections and project it back into the beginning of his discussion in order to found a system with self-consciousness as its ground. This step was, in Schelling’s estimation, the essential mistake of Fichte and Hegel.” Schelling’s superiority to Hegel comes out in several works, but probably the most decisive is in his philosophy of art completed way before Hegel’s which is undeniably a masterpiece and superior in style and historical surveying than Schelling’s (see Hegel’s Lectures on Aesthetics, 2 vols.). But that does not mean we can overlook the fact that Schelling does not provide some absolute perspective by which we can rank the philosopher against the artist, or the prophet contra the genius for all time. Rather, as David Simpson notes in the forward to Scott’s translation of Schelling’s philosophy of art lectures, “Schelling’s idea of the history of art is not founded upon a naïve progressivism of the sort that underlies Hegel’s alternative model (sophisticated as it is on its surface). It is in this sense closer to a secular, twentieth-century notion of history, according to which things are simply different at different times, without offering evidence of some totalizing pattern evolving with the passing of time” (Schelling, Philosophy of Art, trans. Douglas W. Scott, Minneapolis: University of Minnesota, 1989, p. xviii). Naturally, the concern arises why it has taken so long for postmodernists to recognize the fruits of Schelling’s projects or to question the superficial appropriations of such a paramount philosopher. You should be commended for asking such an important yet delicate question and I have a lot more to add on the subject in a forthcoming article on the power of negation.