Don't know if this has been suggested but rather than a rock, paper, scissors approach, How about ranges on weapons. Seems to me missles should be longest range. Maybe counter that by modifying power. For example Missles would be longest range and least powerful. Projectiles would be medium range and medium power. Energy weapons would be shortest range and greatest power. I'm not a programmer so I don't know how hard this may be. It might spice up combat though.
Ed