It all depends on your match. Are you looking to play rock-paper-scissors with your opponents, or are you looking for well-rounded ships to handle any situation? Against the AI, nothing really matters. It is only an issue against other players.
However, if you really want a single style of ship for any scenario, your best bet would be to specialize your offense, but balance your defenses, and then send your ships out in groups divisible by three. That way, you can balance one of each kinetic, beam, and missiles to cover each other's deficiencies.
Ships with balanced defenses cannot do anything against a ship with specialized offense because 2/3 of the balanced defense becomes useless in a one-on-one fight. Armor and Point Defenses does nothing against beam weapons (even though realistically, armor should provide some defense), so the defensively balanced ship is not going to have enough beam defense to protect itself as a result of splitting the hull's capacity with the other defense systems. On the other hand, it is never a good idea to specialize your defenses if you can afford it because it is much to easy to build ships to counter your specialized defenses.
