Perhaps you could have optimal target size for each weapon, and apply penalties when firing at targets outside that size range. That way your 3000 damage anti captial ship cannon would be useless for taking down fighters.

Also what about having a number of tactic slots that can be set each round? You could have tactics like target engines, target point defense weapons, evasive maneuver, strafe, etc... The higher the move tactics and rounds you can plan for.

These could be especially powerful when paired with the right gear. For instance stealth and the right tactics might let cripple the enemy before they can strike back.

Good point. To further this the players have no control over who they fight, they basically enter themselves into a combat pool and then the server matches you up with another player, figures out the combat behind the scenes and the determines a winner (I'm also developing some post-combat stats you can read to get a better idea of what happened in combat). So while players will have a good idea of how their own ship will operate, they can't really predict combat 100% in advance since they don't know what kind of ship they will be up against.

Then players will complain about the matchmaker pitting them against bad opponents. It's random, but in a different way. It becomes a matter of figuring out the distribution of builds, make one that counter most of them and pray for some favorable matchups.