In the course of rewatching the series, I'm realizing that above all else, what separates a great episode from a terrible episode is, to me, how the main characters are handled. Mulder and Scully are brilliant characters, brilliantly portrayed, and the best episodes both hold true to what we already know of the characters and expand them, providing even deeper levels to them. Monday, Bad Blood, Triangle, The Final Repose of Clyde Bruckman, even a bit of silliness like War of the Coprophages, make the show about more than a shooting gallery of paranormal creeps or an overarching mythology series. In those high points, it's a show about these two fascinating people, and how they respond to their extraordinary circumstances, both as individuals and in their relationship to each other.
The majority of episodes are neither really here nor there; they have their story, and things happen, and the good guys ultimately prevail, and we have fun and say "What a great show" and get ready for next week. But we don't remember those episodes when we're making our lists, because ultimately they're all the same. The details differ, but the broad strokes all look the same through the Gaussian blur of our memory.
In the worst episodes, and I still count The Field Where I Died among them, the characters are betrayed by the writers. Whoever was scripting that week (James Wong and Glen Morgan, I'm looking in your direction...) had a story they wanted to tell, but to fit Mulder and Scully into it, they had to warp them beyond recognition, turn these eminently familiar characters into strangers in order to fit the plot of the week. First Person Shooter rang untrue to the characters in every way. They even got the fucking Lone Gunmen all wrong. And this is what I consider the biggest failing of I Want to Believe, greater even than the forgettable plot, that I never for a moment believed that these characters being played by David Duchovny and Gillian Anderson were actually Mulder and Scully. Not for a moment.