Yes, I do agree that X-Files and its near end run had many many issues. I think the out of characterness of it all and the shipping aspect of it were side effects.

It really does depend on the story, doesn't it? Some shows it works for and some it doesn't. But even then, it's subjective. There are some shows I feel it flat out doesn't work when others feel it's fantastic and should be explored more.

Fandom is interesting like that :)