I voted MOTW, although it really depends on what point of the series we’re in. For the first 4 seasons, I loved the conspiracy episodes more, but about the time of the first movie it became obvious that the truth wasn’t out there and Chris Carter and company were just pulling stuff out of their asses as they were going along. Worse, the conspiracy episodes fell into a formula of “introduce a bunch of new questions, resolve one previously introduced question, kill minor recurring character”. The predictability of the deaths became laughable.
When Deep Throat was gunned down at the end of Season 1 I was shocked. Major characters don’t just die on TV without some massive foreshadowing. When Mulder’s father was killed in Season 2, I was dreading it, but I was still surprised when it happened. By the time Agent Fowley was killed, it was so rote that the writers couldn’t even bother to set up a suspense scene, and killed her off camera and mentioned it with one line of dialogue. It was like “Oh shit, we just finished a multi-part conspiracy episode and forgot to kill someone…Hmm…how about Fowley…better tack on a “By the way, she’s dead now” line in the last scene”
So in the later years, definitely Monster of the Week.
I watched X-files regularly from Season 1/Episode 1to about the middle of Season 3. While I always liked the idea of the “Grand Conspiracy,” I never thought they carried it off very well. The arcs were too convoluted to make much sense if you missed an episode or two. Mulder and Scully were well written characters who, with the show’s opening, could make you understand the basics. The MotW let you concentrate on the stories, the Grand Conspiracy made you concentrate on the tale as a whole. Not a bad thing, if well done. IMHO, it wasn’t well done.
Also one of my favorites, along with Humbug (Scully eats the roach, crazy puzzle tattoo guys) and Post-Modern Prometheus B&W, Cher-lovin’ monster). Although I have fond memories of the stand-alones, the mythology was such a lovely backdrop for the development of that partnership. I guess since I’m a 'shipper I loved any episode that built upon shared history, and the stand-alones were usually not good for that (exception for Gillian Anderson’s great All Things).
I’m going to restrain myself from ranting about other shows here, but it seems fairly common for non-comedic TV shows to start moving away from “this week another problem of the usual variety” episodes to bigger story arcs…which they often fail to handle well. There are definitely exceptions, but it seems to me that the arc that starts strong but fails to resolve itself in a satisfying or even coherent way is far more common.
Why do the writers do this? I can understand not wanting to get into a rut doing the same thing week after week, but arc episodes can wind up being just as repetitive. And if your viewers like the basic formula of your show, why mess with success? Why drive away new or irregular viewers by making episodes that are impossible to understand on their own? Above all, why plow ahead with an arc that isn’t well planned?
Like many others in these threads I found the earlier mytharc episodes of The X-Files intriguing, but they just kept dragging it out. It didn’t seem to be going anywhere interesting, it just got more and more complicated for no good reason that I could see. When I realized that things had gotten to the point where missing one episode meant I’d be lost the following week, I stopped bothering. My youngest sister was a huge X-Files fan so I’d still see it occasionally when I was at my mother’s house, but if it didn’t look like a monster-of-the-week episode then I’d go do laundry or something.