Well, I think the whole problem is that the AI is written to support the sexp system, not replace. It is, in game terms, possible to get an Orion to take down a Sath, purely by waypoints and sexp's, because the AI is relying on the sexps to point it in the right direction.
Theoretically, it's possible for a Fenris to take down a Sath if it stayed in the blind spot (For about 6 hours), the AI relies on the mission designer to avoid situations like that.
I suppose as far as Capships are concerned, FS2 was not designed for cage-matches, it was designed for scripted scenarios, and without some really major renovations in the AI, that is the way things will stay.