Time for my regular completely unreasonable gameplay suggestion:

A new set of components for warships designed specifically for punching through defenses. It'd add another set of stats for ships and fleets, in addition to attack and defense, boosted by special components. The counter defensive components would serve the purpose of nullifying the target ship's defenses in the given category. One way that this could be done is simply reducing the defense rolls of the target whenever a ship equipped with counter defenses makes an attack. Another way, one which would make an individual point of counter defense very powerful, is that counter defenses could strip a target of x points of defense in the same way as an attack can, except without doing damage... in that manner, an entire fleet would benefit from one ship loaded with counter defenses.

For nullifying armour, you might have some kind of spacial disruption component or a kind of micro-meteorite machine gun that prematurely cooks off reactive armour, or even just armour piercing shells. Nullifying shields would be a line of shield disruption or distraction techniques, and nullifying missile defenses could be dummy missiles or other such techniques to overwhelm the point defense.

What this would do is toss up the ship balance a bit and allow more of a rock-paper-scissors dynamic in ship combat. Defense heavy ships would counter attack heavy ships, but their defenses would be rendered useless by counter defensive equipped ships, which themselves wouldn't be able to compete as well with heavily armed warships.

More importantly, though, it allows another way to counter an opponent that is ramping up on defense techs (which, to be honest, is already incredibly easy due to the cheap cost and quick research of those components) without having to switch to a new line of weapons. If the techs were a bit more expensive than the defense ones, it could work very well.

At the very least, it WOULD make things more interesting.