Special Items (magic)?

I have also thought about having a 3rd type of ship slot that would be for items like this. Mostly it would provide minor to modest static bonuses that you can use. Targeting Computer boosts all accuracy by 5. Repair Bot adds a trickle of repair to that ship only. Hardened shields redirects 20% of missile damage to shields. Expansion Field makes teleport work on the whole fleet, everyone keeping their relative positions.

You could also have a handful of 1 shot items like described above with a significant effect.

Or some items that have a more modest clickey-effect which would help increase the interactive feel of fights. i.e. Warp Field that boosts your fleet's movement speed by 2x for 10 seconds, with 1 minute cooldown.