I like the idea of Emissive Armour actually turning away some damage. Remember the Excalibur in the Crusade series? Deflects 90% of incoming weapons energy. I would give my right arm for a ship like that
And as for the Vorlon-enhanced main guns, well..... I think there's enough weapons already in the game that you could pick to represent those, except they don't have the after-effect of killing ship movement for the equivalent of a minute.
I think there should be additional tracks on the Chemistry tech tree to allow for new types of alloy which would either introduce new armour types, or enhance existing ones. For example, you could use a thinner armour that allows for more space inside the ship's hull, but provides the same protection as a much more primitive alloy. And costs more
