(“But Elizabeth! They let me fly their ghetto-tastic fighter plane! How was I supposed to know they were evil?” “The fact that they were researching chemical warfare didn’t tip you off?” “Well, maybe, but… airplane!!!”) That's... just truly brilliant. In no small part because it's more than half way plausible as something that could happen on the show.

And as for the wish fulfillment thing... yeah. I think you've got it pretty much spot on there- and it extends even beyond slash. Look at how many deeply geeky series revolve around a set of characters that are in some way separated from their original families, who then proceed to make their own little (geek) family. Like you said, Atlantis is a good example of this. Angel, Firefly, and Magnificent Seven all work well too. Actually, come to think of it, the January series is probably the ultimate example.