Hmm, interesting. Because I watch NCIS almost entirely for the character drama (everyone, even Ducky, seeking Gibbs' approval endlessly, to use an example that seems to have made the jump to fanon), and my impression of fandoms that stick is that they typically have strong character relationships. To give an example, I can only imagine that if one were to slash Gibbs/Tony, it would only be made more interesting by engaging with the former's almost pathological need to protect and nurture the women around him (indeed, his need to do so consistently overwhelming any desire for or chance at romance), and the latter's similarly extreme need to "pick-up" (but not retain) almost every woman he meets (to call back to the dawn of the pastime, Cpt. Kirk).

I'm making the case that NCIS canon is perhaps more relevant to fanon (especially romance-oriented fanon), than that of, say, Supernatural, in that in NCIS the circumstances remain similar, but the character's relationships develop, while in Supernatural, the circumstances develop, but the core relationship has remained fundamentally the same over time (not to say that the relationship does not drive the show).

Oh, and McGee/Abby is canonically liminal and over, but called back to periodically in interesting ways, mostly dealing with McGee calling back to it, if not pining.