It's silly to introduce options that include only one right answer. In the OP, ships would simply use a composite of armour types over their surface, and for the other suggestion of custom weapons... well not only does it not make sense (5kT of death is just that, I don't care what your name is) but its simple 'this is better' proposition, and brings no new tactics at all.
What we really need is an armour model. Orion has huge areas unarmoured, for instance; smacking bombs on that should be far more effective than landing them on the huge armour plates. But then I want a proper subsystem engine, where each weapon has penetration, each subsystem is a volume inside the ship, and ships get disabled long before they blow up. They can do it in UT2k4, for chrissakes
