The point of Season 5 was to shake things up, mix things up, and make them more...
interesting complicated!
On one level this actually worked very well. The "Rebel Colonists" subplot had been bubbling away in the series' collective unconscious for a long time - at the very least since Colony back in Season 2 In Season 5 it would finally be announced officially. Suddenly the baddies stopped being mere baddies and became what Alan Rickman would have called "interesting people". The arc words "Resist or Serve" gave the series a moral dimension it had never really had before - apart from the simple honest pursuit of truth in the face of government cover-ups, of course. Finally, good and evil would get to dook it out in an exciting, ethically complex, er, Grey area.
In another sense though, it was the beginning of the end. The joy of The X-Files had always been that the nerdiness was baked into the format. "World-building" was part and parcel of what the show did. Mulder was our chief geek, painstakingly putting together the pieces. Scully was there to make it all feel scientifically credible (and sexy!). So, to have an actual man in black walk straight off the set of JFK and start spilling the beans - as one does in 'Redux', and as the Well-Manicured Man does in the film - was dramatically problematic. More importantly, it opened the door to resets, retcons, and "soft" reboots that would ultimately allow Carter and his friends to tear up the show's entire back-story into little bits and leave long-term viewers of the show (never mind the unfortunate "fans") feeling desperately frustrated and disappointed.
And unfortunately that undermining of the show's format started straightaway. And it undermined Mulder as well. Having Mulder become a sceptic should have worked in the same way as making the Well-Manicured Man complicated and interesting could have. In practice though, it was a step in the wrong direction in much the same way as giving the Smoking Man a speaking part had been. Mulder had always been clever enough to ask the right questions. He didn't need to start "doubting". Scaling back the mythology didn't make the show more grounded and gritty. It just made it more boring.
Another thing that didn't work on any level - in terms of character or "thematically" - was contrasting Mulder's growing scepticism with Scully's awakening "faith". Carter's thesis that miracles are part of "the unexplained" was twee when Arthur C Clarke had first pushed it back in the 1970s. By the '90s it was positively icky, and hardly worthy of The X-Files.* Which is not to say that stories about psychic abilities and magic could not make for good MOTW episodes. But the supernatural needs intellectual back-up (whether it be esoteric, or theological - or both!) just as much as the extra-terrestrial, and a lot of the time the writers just weren't prepared to put in the research. For the devout as much as for the scoffer, having "God" be the solution to the week's mystery was all too often deeply cringe. And perhaps even more importantly (and without being judgemental), Scully frankly never became Catholic enough to make her religious reversion arc work on a character level.
Nevertheless, for the most part the stories and the arcs both tick along entertainingly and engagingly enough. The revelations about Mulder's family feel forced and hollow. ("Fox and/or Agent Spender, I am your father!" is too Star Warsy not to be cringe.) But the snobbery at the heart of the Smoking Man's rivalry with the Well-Manicured Man and the creepy homo-eroticism at the heart of Mulder's with Krycek both feel right (i.e. wrong) and true. And whatever you might think of the increasingly convoluted backstory of all the things that have been done to Scully by this point, Gillian Anderson somehow manages to make it feel real - and frightening!
*In one of the spin-off comics, Mulder and Scully even get to investigate the Third Secret of Fatima. Heaven help us!