As for modifiers : IMO some should be represented by special facilities, as Kwok proposed, but others, such as trade capacity of Ferengi (so increased trade revenues + maintenance reduction+ natural merchants !), or cunning of Cardassians, have to be racial modifiers...
Armor : in Trek world there's no real armor IIRC, so they should be rare... but I'm more of a TOS and SFB guy than a TNG one, so ...
