Fleet Formation has been programmed.
When a system has been clear of hostiles, you can enter the Command Fleet Mode (default key 'M') then press the Fleet Formation button in the bottom left corner of the screen. This will enable you to change the formation of your fleet as you see fit.
This feature is a prerequisite to the upcoming Shipyard systems, which will enable the player to purchase new ships for their fleet. It will also give players an edge on battles in which the fleet gains initiative.

Initiative will be important for all encounters, and will be determined by the procedurally generated events the player fleet encounters, as well as soon to come systems that the player will be upgraded. Upgrading sensors, engines and recruiting more powerful psykers as crew members will increase the chances of the player gaining favorable intiative.

Initiative, after stats are calculated will go to one of three different types:

Ambush - The fleet has been ambushed! The enemy fleet attacks IMMEDIATELY. The player fleet must wait 10 seconds before it can return fire.
Equal Engagement - Both fleets are surprised by each other, and both will open fire in 10 seconds.
Favorable Battle - The player fleet takes initiative and fire IMMEDIATELY! The Enemy fleet must wait 10 seconds before returning firing and launching fighters.

More to come!
-Artificer Cascadia