Well, I have the impression that the capship battles of WC3 are indeed somewhat scripted.
But on some instances, true combat occurs on the game engine. On WC2, we the capships fighting with everything they have on different occasions. Both the destroyer and the concordia with different Kilrathi vessels.
On WC4, the "Outrun Ella" mission is quite impressive. If you don't take them out, the Intrepid will engage head on all three confed capships. It’s odd that they will only fight with the laser turrets – as the Fralthi vs Fralthi battle on WC1, but it’s impressive nonetheless.