MrDisgusting, don't take this the wrong way, but I don't want folks to get the wrong impression about this film. Having watched this site a long time, only now have I felt compelled to register because I feel it's just that pressing I set the record straight about this film. Your opinions are valid, and your own, but I loved the film, and having caught the first showing at my AMC last night at 12:01AM with little more than a dozen other hardcore X-philers, it hurts my heart to think how poorly this film is likely to do.
I can't speak for production troubles they may have had, as I don't know about them, but I thought the screenplay was fine. Certainly there were parts that may have wanted tweaking, but for what it was, they did fine: Mulder's sardonic wit and general badassery has not diminished since his retirement and the story was pretty creepy when it wanted to be. And as for Mulder and Scully's relationship, the film can only be so stand-alone when it's got 9 years of the show behind it, and since we've seen Mulder and Scully make out before, and know they must have porked to have made a kid, I don't think there was much else to say in the film about this thematically. Personally, I'm glad they glazed over it because I never really cared for that facet of the show. They were doubtlessly finally acquiescing to the "shippers," folks who wanted to see Mulder and Scully hook up, but every other pair of lead characters in every other show ever has done this and I just don't think it's something to linger on.
Father Conelly's solving of the case I don't see as a plot hole because it introduces no narrative inconsistencies and it's not unprecedented that a medium/psychic/ghost, what have you, has solved an x-file. I don't think the greater emphasis should be given to his part of the narrative all the same and as many different strands of the story as there are, I can overlook something like this without being asked to.
Further, the characters have been developed over the course of 9 years, and we've had 6 since the last time we checked in on them, so they can only allot so much time to bringing us up to speed. As for Scully's skepticism, she's been a believer since season 7.
I can understand why you, and probably a lot of other people would not care for the film, though. The film isn't a sci-fi, a horror, an action flick, or drama and none of these elements are terribly prevalent. This film is about the characters. All the hype about it being a "monster-of-the-week" film, I think, gave a lot of people the wrong set of expectations to enter the theatre with. Frankly, I'm not disappointed that they didn't follow the old format (first victim, Mulder's slide show, Scully does an autopsy, yadda yadda yadda), because I don't know how well it would have translated, particularly after this much time and this many changes to the premise.
I thought the cinematography was great and the setting and atmosphere were phenomenal and really set the ambience. The direction was excellent, and, though not immediately apparent, was in usual tasteful X-Files form (for instance, and abduction scene that is mainly shown in a long shot with both characters obscured from view by a truck). The reason the X-Files was seldom hokey in spite of its outlandish premises was this careful omission. Mutants and dismemberments taking up much screen time would strain suspension of disbelief, and these things never look as good as they should anyway (although I think these things are what a lot of people are looking for and will be disappointed by the absence of).
Of course, David Duchovny is not the paradigm of male hawtness he used to be, and some of the extraneous storylines could have been omitted. Also, I wouldn't have objected to further explication as to how the cliffhangers from the show had been resolved, but there was more than enough to love about the film to compensate and the treats for devoted x-philes were deftly enough woven in. I was worried more than most that this film would suck, but I think Chris Carter did a fine job given his means. That said, please, people, go see this movie, so they'll make another one!