Fringe definitely handled the continuing storyline much better. The way they blend in, then transition from, the monster-of-the-week format is excellent writing. It did put a deadline on the story, something which the X-Files writers seemed allergic to as the series began aging.
Worth remembering that both the X-Files and Babylon 5 premiered in the same year (1993).
TV science fiction was just beginning the transition from "monster of the week" to season+ long pre-written plot arcs.
Twin Peaks was only a few years earlier (1990), which pioneered(?) bringing the hitherto only soap opera and family drama continuous storyline to other genres.
TNG is indicative of this too, with the adaptation of season-long plotting between 1-2 (little), 3 (some), and 4+ (more).
Which is to say when the X-Files premiered, having a series-long plan of any sort was still a novel idea in TV scifi.
https://www.imdb.com/title/tt1119644/