I'm still not 100% sure what to make of last night's episode either. There definitely did appear to be at least a mild form of "retconning" that happened throughout the episode. To play Devil's Advocate (because I want to believe that these episodes will be good):
They had to address the lack of evidence that we have in our modern world for the aliens. I'm pretty sure that there was far more "evidence" of aliens being real back in the nineties and before (before everyone had a camera with them 24/7) than there is now. As such, this has led to Mulder questioning his own experiences more. One line from Mulder that stuck out to me was (paraphrasing), "No, I want to believe, but surprisingly hard evidence has been hard to come by." I interpreted this line as Mulder stating that he still believes that aliens are out there, but is also admitting that, realistically, there should be far more evidence for their existence in the year 2016 than what we have.
I agree that Scully's characterization did not feel consistent with where she was at the end of the show's run or even the 2008 standalone film. I can only hope that this will be better explained in upcoming episodes. We still don't have all of the details about the "falling out" that Scully and Mulder had.
Mulder's behavior toward Skinner also felt out of place, although, in the context of the episode, Mulder seemed to believe that his entire time working on the X-Files was a waste. He believes that his entire relationship with Skinner has been built on lies, and he's so one-track on his goal that he ignores all of the evidence to the contrary (which is typical Mulder behavior).
I hope that this is what might actually be getting set up: It sounded like Scully played some part in diagnosing Mulder with depression/and or some other mental illness(es). I think this has potential to be very interesting if it's explored properly. The idea that Mulder has been in a state of self-imposed isolation, and perhaps Mulder (and the people around him) have some fairly serious concerns about his mental health. While there were often throwaway lines about Mulder being "crazy" or "insane" in the original series, I don't remember it ever being something that was seriously questioned outside of contained stories. I think it's fitting that in 2016 Mulder's behavior would been seen as being much more problematic and perhaps have a more sinister implication behind it. I think the Trust No One theme, with Mulder questioning his ability to trust himself could make for a good arc.
One of the more problematic issues I had was that fact that after all these years Skinner is still just the Assistant Director. Talk about being unable to advance in the workforce. (mild /s)