aesthetics wise, I'd go for the advent capital carrier. it just looks so sleak and the side beam weapons just look awesome.
gameplay wise, I'll be totally creative and go for the egg. it can colonise, has a nasty direct attack ability, can stop fleeing enemies from jumping to phase space and the utlimate helps attacking planets, which means less need for the horrible siege ships.
though of course, most, if not all, capships have their advantages and disadvantages.