The second movie was a bit confusing IMO. In the TV series finale, they're clearly on the run and the aliens/supersoldiers/Toothpick man or whatever are sort of still in control, but in I Want To Believe Scully's using her real name in a hospital, and they're given a full pardon...and we never really found out what happened to John, Monica and Gibson.
They probably figured that not enough people would remember or care how things left off in the show for it to be worth the effort addressing those things....and they were probably correct since I have no clue who those three people are. Still, that in itself should have been a warning flag when the made the movie and probably a good indicator as to why it was just so forgettable.
IMO the show lost it's spark *way* before the end. I'm not sure if it's due to Carter running out of ideas or the main cast loosing interest in their roles, both or something else altogether. Honestly just getting Mulder and Scully back for one more random adventure doesn't appeal to me. I'd much rather they do something new in interesting or not bother at all.
I sort of have the same opinion of the recent 24 mini season. While it was fun while it lasted, I instantly forgot just about everything about it and have no particular anticipation for another instalment.