Once a player has earned their stripes in the early game grind and reached some predefined set of achievements, they are proffered a rank (such as Admiral, or something more fitting) that allows them to commission an AI Naval fleet, and a range of auxiliary facilities for remote operations. The player must register a faction to begin.
The remote auxiliaries serve as collection points for commodities, materials, technologies, credits, and exploration data acquired by AI pilots as well as human players. Depending on the type of auxiliary, it may also serve to augment certain activities, such as a Mining facility with appropriate outfitting and defensive capabilities. This is what I imagine the new Support Vessels will be used for to some degree, though the details are still pending at the time of writing this. In this envisioned implementation, such vessels/facilities won't be permanently tethered to a fleet carrier, in that they can be left on location if the fleet carrier jumps elsewhere.
The AI Naval fleet can be configured according to the player's requirements, to perform functions such as mining, missions (specifically courier, cargo, and passenger transport missions only), player-defined trade runs, and player assigned combat/defense roles. Bounty hunting, pirating, smuggling, exploration, search and rescue, and all mission types other than courier, cargo and passenger transport should remain the sole province of direct human player intervention.
To picture how this would work, think back to a classic RTS like Starcraft, where SCVs collect minerals and vespene gas, but in this case it's materials and credits. Your AI mission runners and trade vessels are like the SCVs, so the first thing you're going to want to do is save up to purchase a small initial fleet of these as your "gold" miners. These will also serve the purpose of increasing your mini-empire's reputation or influence with the factions of your choice, according to your strategy, as well as affecting the commodity market. So you send the trade vessels off on predefined trade runs for specified commodities, and the mission runners will accept any of the three specified mission types at the stations of your choice, with any additional parameters you're able to set. Those ships will continue on that way until told to stop, or until there are no more applicable missions, or they're destroyed.
Next you could purchase a mining Support Vessel, and a fleet of capable mining ships. Unless of course your base station (provided that feature is introduced) is close enough to the mining site to collect materials, in which case you could forego the mining Support Vessel at first. Once you've directed your miners to work on a particular site, they go back and forth also like the SCVs until they're told to stop, or until there's nothing left to mine, or someone destroys them. Like NPC Fighter Pilots, all AI pilots will have ranks, which will increase with experience, and it will be specific to their activity. So a mining ship AI pilot will get better at mining over time. This will translate to better being able to identify specific deposits, better success with detonations, and faster collection.
Somewhere in between these, you'll be wanting fighters to defend your credit and material miners. So you'll purchase these when you're able, keeping in mind that each AI pilot you hire has an ongoing cost which increases with rank, so your revenue must be greater than your expenses in order to keep them employed.
Eventually, you'll be able to amass a significant combat fleet, and use it dispersed across your assets for defense, or gather it in one spot for an epic battle. You will be able to allow the AI to fight unguided, or direct them through an interface built for this feature, and even directly take part in the battles yourself.
Starcraft also had a unit limiter which varied for each race. For Protoss it was PSI through Pylons, for Terran it was Supply via Depots, and for Zerg it was Control via Overlords. This should also be a factor for control and balance. For example, each auxiliary Support Vessel you place should give you an additional X capacity for supportable units in your navy, and there should be a limit on how many Support Vessels you can have.
Admirals can employ their faction and squadron members in their navy, and delegate certain organisational tasks to them. They should also be able to create and customise missions in systems they have influence in, particularly things like assassination, bounty hunting, and new mission types for disrupting mining and trade operations of other Admirals, with set limits on rewards of course, which are only given after the mission is completed. This is for targeted strategies and espionage.
I also think that Capital ships should become available to a player who has reached this rank.
So effectively, the Admiral employs a strategy to gain influence for their faction, and spread it to the areas of their choice, which could bring them up against other Admirals, which could trigger a war, unless players take a diplomatic initiative. How this could work with PowerPlay is either that the Admiral is in direct competition with the existing Powers, or else they become a significant vassal for a Power, such that the player's influence is added to the Power's influence, which could have its own benefits (resources, additional ships, etc). I'm not too sure on that front, as I'm not that knowledgeable in PowerPlay.
Admirals can of course still pilot their own ships and play as they always have. This is more of an optional end game dynamic, but it also provides other commanders with new play opportunities, to join in the wars as members of a player empire, or to work freelance on missions for any sides in a conflict. There could also be AI or Frontier controlled Admirals thrown into the mix.
With the introduction of fleet carriers, most of the major pieces for this idea are already in the game. The BGS would have to be improved some more to cater for the new dynamic, and interfaces would have to be designed for the Admirals to control their fleets and other assets, create custom missions, monitor progress, and to allow them to direct battles, but I don't believe it's as drastic as it may sound.