The aforementioned fighters can be utilized in battle if you install fighter bays on your ship. Each fighter carries different weapons with a tradeoff in speed and cost. Other special systems that you can use are minesweepers, repair drones, and colonizing modules. The joy of ship design is diminished when you consider the limited technology in Pax II . There are no cool special systems like cloaking devices.
Weapons are likewise limited.
In Master of Orion II, you could customize weapons to have different properties so that you could have a variety of specialized ships. The weapons and devices in Pax II are generic in comparison. Combat is handled in a timely fashion. Ships line up along opposite sides of the 2D battlefield and then clash together in glorious real-time fashion. There are several commands that you can give besides the usual 'move' and 'attack'.