They should have different race pics.
Seriously though, Instead of giving them bonuses, why not give them faults?
Focusing on ships:
Organic race ships shouldn't use anything mechanical, unless they're grafted or something. (Ie: You wouldn't like to live with a painful, scorching, and heavy PPB for an arm.)
Magic races should eat up a lot of supplies. (Ie: it takes a lot out of you when you cast a vanishing spell on a starbase.)
Physics races shouldn't have bonuses.