The ancients wouldn't really be much more advanced than Terrans or Vasudans - don't forget they were wiped out by the Shivans, whereas the GTVA has thus far managed to survive. As far as I'm aware, it was a Lucifer fleet that destroyed them (they found out how to track it through subspace to bypass it's sheilds, but by that time they had lost their entire fleet, and so had no way to attack it), although the war may have been rather protracted, with the Lucifer only appearing late-on - perhaps after the Ancients managed to destroy some of the Demon-class destroyers they had already encountered.
I think an ancients campaign could be interesting - there are some Ancients mods around, particularly in the Inferno campaign (though some are, erm, a bit crappy) so it is feasible. You'd have to have a serious redesign of the interface, HUD and weapons, though, and one hell of a script-writer to make it any good...