I'd like to make a suggestion about beams. Perhaps you could take a page out of FTL's book and make it so beams only penetrate if their damage is higher than the shield's health at the moment of impact, but they don't reduce shield hp. I don't remember if I've seen any beams with individual damage higher than 1, so maybe it would be if the collective damage of all beams hitting the shields at that moment is higher than the current shield hp, or the collective damage of all beams hitting the same level of the shield, not just anywhere on the shield, is higher than the shield hp at that time, the beams penetrate (or in case #2, just beams on that level) but still don't damage the shield (unless, of course, the beams destroy a shield generator) and maybe even, like with FTL, they loose 1 point of damage they can inflict for each "layer" (shield hp) in the way of the beam. This would potentially fulfill your thought of making them not damage shields, but also perhaps be slightly more logical, since a shield would logically not be able to stop a weapon more powerful than itself, just reduce the damage. In other words, you could damage a shielded enemy if your beam attack was more powerful than their shield, but not with the full damage of an uninhibited beam, and it wouldn't outright leave the enemy unprotected against normal, more direct weapons that can't just have their energy scattered like a beam. Even lasers couldn't, since from a realism point of view, for beams and lasers to travel at different speeds, the laser is probably more akin to a blast of ionized gas.