[Suicide Junkie]

The empirical evidence in CBmod does show that you *can* make the specialized designs come to dominate... but its not nessesarily easy.

The important point is that you have to set up the underlying physics carefully; all the roles have to be of roughly equal importance. (Focus on balancing point defense, leaky PD too, in order to keep missiles fighters and ships all useful throughout the game.)
The weapons that are good for one should be mostly incompatible with use in the other roles. Not only the weapons, but engines, and defenses too.
It helps to allow things to take up huge amounts of space. A good anti-ship weapon could take up 80% of a fighter, naturally leaving you with a slow, lightly armored bomber design.
The best anti-missile weapons could be short ranged, thus requiring powerful engines to intercept successfully. Engines taking up half the space on your fighter, plus the guns, leaves little armor.
And if you want a fighter that can stand up to return fire, you'll need moderate guns and a moderate engine, giving you a dogfighter.

In SE5, you have the additional dimension of shot speed to play with, but you lose the weapon-stacking mechanism.


Its not easy, but IMO, it is worth it.

PS:
Would you like to play a game of CBmod to see the theory in action?