In AI vs AI fights in each class, I always recall that:
A Confed patrol ship would nearly always beat a Manta, simply because it had an extra missile.
A Confed Frigate and Rebel Destroyer would have an extremely close fight, coming out something like 50/50. It generally came down to who landed more torpedos or heavy rockets.
A Confed Cruiser would pretty much always beat a Rebel Cruiser, because it had way more shields and the AI makes poor use of the Rebel's superior maneuverability.
In the hands of the player the two Rebel capital ships were generally better, I found - but the AI in the original EV was so thick that it nearly always came down to pure firepower/shield strength because they'd generally just unload all their secondaries then conduct repeated head-on firing runs on each other til one was dead.