Bah! Bah I say to all of you!
I loved that show... I was pissed when Mulder went off in Season 7 or 8, but he came back.. I don't know, maybe if I were waiting week-to-week as others may have been, to see if he came back, and then found he didn't for a whole year, I'd be more pissed, but I was able to just watch them back-to-back. That maybe why I'm more forgiving. I actually liked the last few seasons of the show, even though it became a big 4-way between Reyes, Dogget, Mulder and Scully. I actually liked Doggett just for his own character - I dind't at first, he was a total dick. But in between the lines there were things I liked. You could tell that when he first met Mulder that even though he had talked a lot of smack prior to that point about how goofy the man was and had all these wacked out, half-baked ideas, you could still tell that Doggett was in awe of him and his reputation as a great FBI agent. Especially later, when Doggett was facing actual X-Files that he couldn't figure out, he kept thinking to himself that Mulder could do it instantly. I didn't like Reyes as much for herself, even to the end, but I still liked the Reyes-Doggett dynamic.
I probably liked the introduction of the "new X-files investigators" probably because the way I interpreted the attitudes and statements about Mulder and Scully from that point on was in a kind of reverence. Reyes and Doggett, and consequently the viewer, was always aware that Reyes and Doggett would never be as good or as quick to figure something out as Mulder and Scully. Reyes has Mulder's openmindedness but never his intellect, Doggett had Scully's loyalty and doubt but never her medical knowledge or Mulder's quick wit. It was always exciting to see when they called in Scully for advice because it was like she was the First Lady of the X-Files and Mulder was the almighty God of the X-Files, the one you always thought "oh Mulder'd get thi sin a heartbeat", yet it didn't compromise the storytelling as a deus ex machina because he never showed up to save the day... which was the saving grace of the story while still being a real pain in the ass right up until the moment he returned.
As for the baby-thing, I can see your heartbreak over that Beth, but I honestly understood her actions because I'm not saying it would be easy, but if you were completely convinced that keeping him with you would only put him in danger, wouldn't you have to give him up? I mean it would be SO SO SO hard, but it would probably be the right thing to do, and in reality, I"m sure as a parent you would just HAVE to be leaning upon a conviction that you will go back for him someday when this is all over, it's probably the only way you could get through it.