I can't vouch for it, but I'm pretty sure the AI was raping even more because I was almost solely equiped with lasers and they had a bazillion deflectors on each ship.
Now I can't say if that was on purpose but I did fuck me up.
A fair number of space 4x games, notably GalCiv, have used the tripartite lasers vs. shields/drivers vs. armor/missiles vs. PD weapons and defense structure. MoOII of course had beams vs. shields/missiles vs. PD/torpedoes vs. jamming, and also mass drivers, and probably had the best implementation of all of the games that have used this sort of structure.
In my opinion, this tripartite structure belongs in the garbage, at least as the primary determinant of attack and defense power. The min/max/optimal range, "projectile" acceleration/velocity, targeting resolution (accuracy vs. different-sized targets), lock-on time, orientation, coverage, degrees turned per second (in the case of turrets and articulated weapons), damage of course, and other discrete characteristics of weapon systems should be emphasized, so that varying sizes and types of ships can fulfill specific roles in battle (AKA, fleet composition and doctrines).
Take a destroyer, for example. In the context of space battles, a destroyer should be fast for its size and mount numerous 360-degree-radius turrets with fast lock-on times, fast turn rate, high targeting resolution, above-average range, and below-average damage, in order to effectively track and destroy several small, fast, short-range attack ships at any given time, thereby effectively defending the larger ships in its fleet. In turn, other ship types can be designed to counter destroyers, fighters can be designed to evade destroyers as best as possible, etc. A large dreadnought might mount a spinal superweapon effective against large, slow capital ships, starbases and so on.
Formations should matter, too.
I'm probably just dreaming at this point, though. Maybe that's a little too granular to work in space 4x, who knows?