I think Chris Carter has said in interviews that he never intended for the X-Files to have a proper ending. Something like "life never ends, why should the X-Files?"
To be fair, "My Struggle IV" has closed off most of the show's plots, just not in a terribly satisfying way. The Spartan Virus isn't coming, the Cigarette Smoking Man is dead (?), the X-Files have been shut down and Mulder and Scully are starting a new family. If it weren't for Skinner being either dead or injured in an alley nearby as Mulder and Scully hold each other, this could have been an ending. But Carter deliberately aimed for the Season 11 finale to feel incomplete. CHUCK and BUFFY have shown how you can write a season finale that works as a series finale, but Carter has declined this route, instead insisting that THE X-FILES will return.
That seems unlikely to me. Season 10 started with 16 million viewers and ended with 7.6 million which is pretty solid, but Season 11 hovered around 3.5 million for most of its run.
I think something is wrong with Chris Carter. He was never the best writer on the show, but some of the decisions that went into this final season (especially the finale) were beyond just bad writing.
I think the problem is Chris Carter's anthology style. His refusal to engage in serialization is mismatched to how a modern viewer watches television.
Chris Carter once remarked shortly after Season 9 that THE X-FILES' audience had disappeared and he wondered where they'd gone. The answer: they'd gone to shows that offered ongoing plot and character development with characters who grew with the viewers.
In the 90s, it was fine for Mulder and Scully to be written with contradictory characterization from week to week and for the X-FILES universe to be magical one week and scientific the next. Most viewers didn't see every single episode. But towards the end of THE X-FILES, television was becoming more serialized. THE X-FILES wouldn't commit to serialization despite the alien myth-arc and Mulder/Scully relationship demanding it; as a result, the audience gave up on the show.
In 2016, THE X-FILES received a second chance and now it had viewers who would see every episode. Carter had an opportunity to serve this new, mainstream audience wanting to see week to week development with Mulder, Scully, the myth-arc and their partnership. But Carter instead presented episodes that contradicted each other from week to week.
"My Struggle" declares that the alien myth-arc is THE X-FILES primary content, but then "Founder's Mutation" offers no progress on delving into the Conspiracy of Men. The Spartan Virus is unleashed in "My Struggle II," but MSIII rewinds time to minutes before the outbreak – and then has it on hold for reasons never given. The Smoking Man is hideously scarred in MSII but healed in III. Colonization is debunked in Season 10 but genuine and aborted in Season 11.
One could argue that THE X-FILES is really about the characters, not the plot, but even the characterization was perplexing from week to week. Mulder and Scully had left the FBI in "My Struggle" but acted like they'd never been gone in "Founder's Mutation." Mulder went from believing in "Founder's" to skeptical in "Were-Monster." "This" had Mulder and Scully living together but "Plus One" had them apart. Later, "Followers" showed that Mulder had never been to Scully's home and had Mulder driving what was Scully's SUV in Season 10. "Plus One" wrote Mulder and Scully like they were still in their 30s and on the verge of becoming romantic while "Nothing Lasts Forever" made them amicable exes who were nearly senior citizens.
Each week, Seasons 10 - 11 found new ways to baffle. Was Colonization genuine or a fraud? Is the show about unravelling a conspiracy or weekly monsters? Are Mulder and Scully living together or not? Is the Spartan Virus coming or not? Are they searching for William or not? Is this universe scientific or magical? Chris Carter wouldn't decide. The result was a show that couldn't even figure out where the characters live or what car they're driving. A show that confused casual viewers like Slider_Quinn21 and broke diehard fans like the EatTheCorn webmaster.
Carter's view was that mandating consistency would deprive the individual writers of their creative freedom. But when even basic character details aren't consistent from week to week, viewers become detached. They can't connect, can't relate and can't get invested. The show went from 16 million viewers to 3.5 million. Alongside FRINGE and SUPERNATURAL, the modern revival of THE X-FILES looked clumsily out of touch. It's time to let THE X-FILES go.