This is expected to be one of the major focal points of the game. Unit combat really provides the only "action packed" moments in a 4X game, so designers really need to put some thought into this. I've decided on several important aspects to ship combat in BDBV:
Real-time - although you will be able to pause combat at any time and give orders to your fleet, the actual combat will be occurring in real time.
Mixed AI/Player control - You will choose which ship you want to personally control (pew pew) and give orders to the rest. These orders could be: a) Retreat, b) Attack Ship X at max range, c) Attack Ship X at min range, d) Assist Ship X at max range, e) Assist Ship X at min range.
Variety of weapon effects - The idea is that your battle tactics will vary based on your weapon technologies. However, you don't technically get to choose which weapons you will learn unless you are willing to continually roll the research dice. Maybe you'll get beam weapons, or maybe you'll get plasma streams.. or something else. Whatever you use, you'll need to adapt your tactics. You'll probably want more than one type, however, since there are defenses that can effectively neutralize certain weapons.
Weapon cooldowns - to avoid button-mashing, each weapon type will have a firing cooldown. Before a combat starts, perhaps, you will be able to choose between shorter cooldowns (pew pew pew) or larger blasts (PEW). Typically, longer cooldowns will give you more dmg/time at the cost of responsiveness.