An idea borrowed from the 4x game Sword of the Stars. Play it. Seriously. Have weapon mounts of different sizes. Heavier weapons require bigger hardpoints, but small weapons can be mounted on a larger hardpoint as batteries of multiple weapons.
It allows a lot more variety in ship designs Want a fighter-defense cruiser? Just drop a defensive laser on one of the big hardpoints. It also stops people loading a ship entirely with the heaviest weapon they can (heavy plasma boats, anyone?) It also makes for interesting choices. Do you really want that heavy plasma, or do you want an array of smaller, more accurate weapons? With the weapons for which it would make sense, you could, rather than having an array, have the weapon simply scale up depending on what kind of hardpoint its mounted on. Cruisers could carry frigate-grade weapons (like, for example, anti-fighter missiles, thankyouverymuch)
It would, of course, require a lot of rebalancing. Defining what exactly qualifies as small, medium, big, and heavy weapons, and making sure their stats scale accordingly.
It would allow very odd things like, say, a cruiser covered in extremely light weapons.