DuracellEnergizer said:

In hindsight, they probably should have

A. Had Scully become significantly less skeptical of the paranormal somewhere around Season 3/5.

or

B. Written some (more?) episodes where apparent paranomal activities were hoaxes/misidentified natural phenomena/etc. to help justify her unwavering skepticism.

Of course, I don't mind Scully's hardline skepticism all that much, silly though it gets at times. My pet peeve with the series is with how poorly the mytharc was developed and executed.

Yeah either one of those would have fixed the problem. I mean I like Scully but at the same time after a while I have to wonder if she has been part of the same story I have been watching. I mean there is being a skeptic and then there is looking at the sky and calling it red,that it what I felt like Scully was doing after a few seasons of something weird happening to Mulder and Scully every single week.

I think the problem with the mytharc is that it was only ever meant to be hinted at when the show was developed,but as it became more popular with viewers it became the focus of the show. From what I understand the show was supposed to be mostly a monster/strange event of the week type show but the mytharc episodes started getting better ratings then those so that is what the writers started focusing on. the only problem is there was no blueprint and there wasn't anyone writer who knew what was going on so it kind of fell apart.

Still it does say something about how good The X files was i think that these problems that would kill most shows for me didn't kill The X Files. I still love the show and just wish certain things had been done a little better but over all it is still one my favorite shows.