Yes, which is exactly why I compared the state of the shows based on where Fringe currently stands: at the end of season 2, preparing for season 3. It makes no sense to compare a show as mythology-heavy as Fringe to an entirely finished franchise. In my opinion, at the end of each season 2, Fringe and The X-Files stand comparatively similar in terms of their respective mythologies.Except that Fringe has even me more answers to the overall mystery of the show in two seasons than The X Files did in 9 years and two movies.At two years into its run, The X-Files also seemed to have a planned storyline that made sense. As much as I am enjoying Fringe, I'm always going to be wary that it will all fall apart at some point.
After watching X-Files a year ago for the first time on DVD, I wasn't confused by the mythology as many people said they were when they watched it as it aired. They seemed to answer all the questions. Maybe over 9 years some details were forgotten making the mythology more confusing? I think it works better on DVD.