The X-Files felt, to me, like its mytharc was heading in a single direction for most of the show's run; it didn't lose steam, for me, until the fate of Fox Mulder's sister was finally revealed in Season Seven, two years before the show ended. That was a mistake, since Mulder's search for his sister had been the underlying personal reason for his quest; after that, things really seemed to deflate. [It should be noted that the individual episode in which Mulder found his sister was one of the most moving of the entire series.] TXF did go on longer than it should have, and like all such things, it started taking on the tone of being made up as it was going along. But it wasn't that way for the majority of its run.
And here's Jayme's comment:
Oh no no no no NO! Mulder's sister episode was the one that got me to stop X-Files, cold turkey. It was NOT the most moving, unless you count throwing things at the screen moving. It so grossly contradicted so much established series continuity that I felt physically betrayed and violated by Chris Carter--not only was he making it up as he went along, he just didn't care. Look, if he were going to go with a non-alien abduction resolution to Samantha's disappearance, then that creepy child abductor/murderer from season 4? Season 5? That would've been the way to go. THAT was a chilling episode. But really, "She's in a better place"? Seven years of buildup for "She's in a better place"? Gimme a freakin' break.
As far as jumping the shark goes, X-Files did it when they wiped out the entire conspiracy at the end of season... 5 was it? Then the beginning of the following season the conspiracy picked right up where it left off, even though everyone "In the know" was supposedly dead (everyone--aside from Cancer Man--might not have been killed, but they never even tried to establish this). Bad, sloppy, careless writing.
And don't even get me started on the loose thread of Mulder's being infected with the black oil. Chris Carter promised in interview after interview that it would be revisited and have a "profound impact" on the series. Then he promptly forgot all about it. Sheesh.
Yeah, I love me some X-Files, but I hates me some X-Files in equal measure.
It seems that we're both in agreement, in a way: we both agree that the resolution to Mulder's quest for the truth about his sister was mishandled. I just happen to think that its mishandling happened in an otherwise decent episode, while Jayme...doesn't. Fair enough.
I don't much agree with the rest of his complaints, though. I found the execution of the entire Syndicate, minus the CSM (who was most definitely shown escaping, as though he'd known beforehand what was about to happen), an inspired plot development. (It was toward the end of Season Six, by the way.) The "Conspiracy" didn't just pick up and keep going; it -- or what was left of it -- had to suddenly retool and reconfigure. This thrust Krycek into the forefront, and made the CSM more of an outlaw (remember, he'd been an actual government official in the pilot, so his descent is quite the journey). I enjoyed seeing "the conspiracy" itself reduced to "making it up as it went along", and as the series went on, it became the mysterious aliens who were setting the agenda, not "the conspiracy". I liked that.
As for Mulder's being infected with the Black Oil, I assume Jayme is referring to the two-part episode "Tunguska/Terma", in which Mulder is subjected to forced infection in a series of experiments by Russians who are attempting to create a vaccine to the black oil. I always assumed that the vaccine was successful, thus keeping Mulder from being "taken" by the Black Oil (which also explains the existence of the vaccine two years later, when Scully is infected in the TXF movie, as well as another plotline later on when Marita Covarrubias is subjected to experiments designed to refine the vaccine). I've seen fan speculation that the presence of the vaccine in Mulder's and Scully's blood somehow alters their DNA such that Scully's baby, born in Season Eight, is a very special baby indeed.
Here's a really good summation of the TXF mytharc. What's neat is that it all works, as far as I can tell, but quite a bit of it is the result of reading between the lines. TXF would have suffered greatly, I think, if the show had ever just stopped to give lots of answers. The answers were always suggested, never stated outright, and as that summation shows, there was more than enough info given to piece things together.
Now, did Chris Carter and his cohorts at Ten Thirteen Productions plan all this from the get-go? Undoubtedly not -- but really, who cares? TXF was always about the journey, anyway.