I was happy, too, that they let Samantha, the "real" one, rest in peace. I thought the story was pretty strong, too, on it's own. I know there is a segment, probably a large one, of the audience that shunned all "supernatural" type elements in favor of "hard science/science fiction" elements, but I didn't mind this switch. I thought it was a really powerful scene in particular when Mulder realised they were standing in the field of graves and then the FBI agents doing the crime scene excavation. Also, for the whole series, anytime Skinner shows up, I like it. I also liked how they were given up on the whole thing as another of Spooky Mulder's crazy connections until Scully made the connection of the hwy sign to the evil Santa village.
That reminded me somewhat of Millenium, you said you didn't remember that one. I watched that one a lot, too. Frank Black was a little like Mulder, a brilliant criminal profiler for the FBI, but he had visions of the murders and murderers and could connect these clues for these horrible crimes to solve them. There were lots of murders, serial killers, mass murders, and other nasty things that he worked on. I didn't see the last part of Millenium to compare the X-files episode to. I'd like to check that out in the near future. I liked the X-Files episode, but it seemed like it was just there to let Frank get his daughter back and the rest was just extra. It may have made more sense if I saw the last season of that show.
Thing I didn't like about this, was after twenty years of refusing to accept the death of his sister, clinging to the alien abduction, Mulder just accepts it here without any significant physical evidence. He just gives up. It would have been fine for a final episode, but there's more X Files after this. What's Mulder's motivation now?