Bar none, the best part was finding that Mulder and Scully's pillow talk consists of toxicology reports and animal tranquilizers. WHY DOES THAT NOT SURPRISE ME AT ALL. (Also? Squee. And heh, their combined paranoia put them in a house with a giant chain link gate out in the middle of nowhere, either in West Virginia or near DC. I was never quite clear on exactly where they lived.)
Did I mention squee above? Because yes, squee. I had heard rumors of a bitter separation prior to the film, and the whole "I won't come home tonight" thing made me a bit faint in the heart, but ahhhhh, that scene in front o their house? WORTH. IT. (Although I did wonder if there would be a bee somewhere in there...) Er, question, though...so Scully says it's Mulder's stubbornness that made her fall in love with him (*cheers*), and he says that's why they can't be together. Uh, they looked pretty damn "together" to me. That was one of several things I didn't quite understand.
In general, the nostalgia factor was VERY high, which was really all I was expecting. Hell, M&S could read the phone book at each other for two hours and I'd watch. Plus there was the Skin-man! I love me some Skin-man. (Also loved the little trick with Mulder's cellphone. BWAH! Although I might have appreciated it more with Morgan & Wong on that list as well, but, eh. Still funny.) I cackled at the bit with the boat in the credits. HEE!
Beyond that...hmm. Okay, the most unbelievable part was that Scully could go from forensic pathologist to brain surgeon in, apparently, very little time. Scully the county medical examiner I would believe; Scully the brain surgeon, not so much. But anyway.
I had always wondered what it would look like when Scully finally said no more, and...I guess it looks a lot like this. (Except without the unbelievable brain surgery. But anyway.) I guess she had no choice after the ending of the series, but...it seemed to work for her? Mostly? Except for the dying kid? (And ow, that "if you were a mother" comment. OUCH.) However, the plot...was not so good. I think it didn't work as well for me because M&S were in consultant positions to the FBI rather than agents themselves. They weren't at the center of the action until practically at the end, and then the whole Russians-and-Callum-Keith-Rennie-sewing-heads-on-and-mutilating-dogs...thing didn't make much sense at all. The psychic priest was supposed to be creepier than he turned out to be, I think. Oh, well.
But plot failings aside...this wasn't about the plot, this was about nostalgia and 'ship, not necessarily in that order, and it delivered on both counts, so I'm happy. (Okay, I would've been happier if Mulder hadn't had that tribble on his face for the first half hour, but, eh. I can deal.)