Good question Matt. It all starts from the carrier and CEX. We have built-in support for carrier communications which are currently unused but will show their teeth with this product. The AI is kept from crashing into one another through a rudimentary set of rules that we'd like to call ATC.
For the player to get in the mix, we will develop a proper ATC & Deck crew system based on real-world procedures. Initially it will offer the bare essentials to comms, but our goal is to gradually expand the available actions and animations with new versions. This system will ensure safe coexistence of the player and AI-controlled vehicles, with each one going about their business. As I wrote above, we are already working on some mission-related behaviours for the aircraft, such as Inflight Refuelling - the AI aircraft shouldn't just do joyrides on and off the ship.
It is a big and ambitious project but will be worth it in the end. We intend to post regular updates on it so keep an eye on our Facebook, Youtube and here (if I'm not spamming

).