Gillian Anderson's unexpected pregnancy was probably not the best way to get a storyline started, but as the outcome is marvelous, her absence is largely ignored and more of an interesting factoid than something that could have derailed the entire show.
"Ascension" is a must-watch episode because it is important to the mythology, but the episode lacks bite, especially after Scully disappears. There is an uneasy tension with Mulder interrogating Duane Barry and his dealings with X, but also little plot. The main thing is, the audience is wondering whether Scully will be recovered by the end of the episode, and having watched the episode before, I already knew how it would end.
On the plus side, Skinner reopens the X-files, having had enough of CSM, Krycek, and the shadowy cabal pulling the strings. Scully's mother, Margaret makes an appearance in the episode and interacts with Mulder, a nice touch to the episode. Also, we learn how Scully is an out-of-practice Catholic, who wore the cross only because her mother gave it to ger. In the grand scheme of things, small developments like this are crucial to where the drama can go.
We learn a little more about the organization and CSM. When Krycek pries for information into Scully's whereabouts, CSM tells him he doesn't need to know, indicating that lower-level workers like Krycek have no clue about the big picture, but are doing the job anyway. Later, after Krycek inquires about killing Mulder to fix the issue, he responds, "Kill Mulder and you risk turning one man's religion in a crusade."
Score: 8.7/10