WTF? I can't believe that the preference for Mulder is that strong. I've actually been rewatching the series recently, and I think that Scully is one of the greatest characters ever to have graced the small screen. I love Mulder, and the whole show generally (pre-Robert Patrick), but I'm way more in love (OK, fine, lust) with Scully than a grown man should be with a fictional character. In the few run ins I've had with celebrities over the years, I've never once introduced myself, nor gone out of my way to talk to any of them (except for Barry Sanders when I was 8 or 9, but that's a whole other story), but if I ever got to meet Gillian Anderson, I would be in full on fanboy mode, unapologetically stammering, fawning and offering my hand in marriage. At 45 I still find her radiantly attractive, and I'm pretty sure it's because of my being glued to the X-Files as a lad.
I feel the same way actually, and can corroborate it with some guy in the front row for the premiere of the X-Files movie that yelled "I LOVE YOU SCULLY" during the titles. Still had to post the article because it was an interpretation I hadn't thought about before.
I think in a lot of ways Scully actually is the hero of the show. She often narrates the episodes, and the show even starts when she is assigned to the X-Files, while Mulder has apparently already been pursuing them for several years. Mulder learns more and more about the "truth", but he is always after what he's after. The story arc is that of Scully, from green agent, to somewhat believer, to mother, etc. Obviously, it's all academic, as the show needed both characters to succeed, but I think the Mulder/Odysseus comparison is not really correct.
I would agree with you regarding that the focal point is from the narrative standpoint, which is Scully. However the most interesting character is by far Mulder. But that's often the case in most stories. Usually, the narrator isn't the most exciting character. I should mention that I've not watched the entire series yet, but I am inching my way through it. -it's great television.