The Victory felt most like home, possibly because WC3 was the first interactive-movie and the characters had more depth. However, strictly based on combat reliability I'd have to go with the Concordia. Because of the impenetrability of her phase shields, any non-torpedo-carrying enemy ships are no threat whatsoever, unlike any other WC game (even in WCP, since some capships components can be destroyed by gunfire.) In fact as far as I can remember, the only time the Concordia can ever be destroyed is during a Gothri attack in Special Operations 1. Other than that you can sit back and let her flak and Phase-Transit cannons take out everyone without having to worry about those "Your carrier has been destroyed" or the ever-annoying WCP "You are unable to land" messages.
BTW, anyone know why it seems a number of friendly capital ships in WC2 are "invulnerable," like Paladdin's Free Trader as well as a couple Gilgamesh-class destroyers (Hector etc)? You can tell when it gets destroyed because (duh) you hear the "friendly capship destroyed" music, but they are still alive. Not gonna complain though....