X-Files has always had a rather dreamlike quality for me. I think it shows in the prose I use in the stories - more detached, darker, with longer sentences and different word choices than I use for other fandoms. This is probably why I used "once upon a time" - these almost have the force of the darker fairy tales.
The stories in the annex all lean towards Mulder/Scully romances. I can see why even as I vehemently deny it. There is a closeness to them that is closer than many romantic couples - it's the closeness that, in traditional male partnerships, breeds slash. You know they'd die for each other; you know that they are so close that any other relationship is doomed to failure. Even slashers know this, so they often make poor Scully a villain, a bitch, to be disposed of or just put her, forgotten, into the background. I've been guilty of the latter myself. The only other role she can play is helper, which is what I choose to do.
I don't think any of the relationships on XF are good for the long term - Mulder/Scully would end up fighting, their disparate world views suffering from too much closeness. Mulder/Krycek has too much darkness, too much blood and danger and violence. Mulder/Skinner or Scully/Skinner has all the problems of boss/subordinate, and the power dynamics of that. Mulder, especially, would have problems with it.
I hate to say it, but Scully/Skinner would work well. She's strongwilled enough to stand up to him, but she has this whole thing about older, more powerful men. Skinner seems to actually respect Scully, which he doesn't seem to do for Mulder. Then again, he cried for Mulder. Melt! So who knows?
I'm not sure I'll ever write it again, but if I do, it'll be about those once upon a time characters who will never live happily ever after.