Actually, this is a pretty interesting approach for multiplayer competitive BH. Here's my take on it:
Each player/team starts with a single flagship. Once someone's flagship is destroyed, they lose, and become an observer if more than two people are playing (Any ships they had would essentially become bounties, and captured planets would return to a neutral state). The map would generate with a bunch of bounties, and all players are free to jump around in realtime. Once all bounties in a sector have been destroyed, it becomes free to be contested, and acts quite similar to domination in that aspect. Each planet grants a source of income, and a small source of FTL fuel, which varies on the planet's original difficulty tier. Planets could either produce extra FTL fuel, or source income; however, instead of the income going directly to your budget, it would be sent towards a 'factory', which produces a ship manually set by the player (Of course, larger ships costing more would take more time to produce). These manufactured ships would be AI controlled, and set to your allegiance. There are three ways that ships can act after being manufactured: Patrol the current sector (default), jump to/protect the flagship, and hunt by jumping into a specified set of sectors (If FTL isn't present, only Patrol would be selectable). Players can view any sector where one of their ships is present (Limited to fog of war if it isn't controlled by them) Each ship can be told to change it's setting via the hamburger menu when selected. It might also be neat if each planet could set up a queue. For instance, you could tell a planet to create 5 fighters, tell them to patrol, then create a dreadnought and send it to the flagship (Possibly with the ability to loop a set of orders).
Pros:
More based on piloting strategy, without rendering ship design useless
Would feel much more in-depth than "Slap a couple ships against each other"
Perfect for lore/RP battles
Possibly competitive
The AI can handle fleets much better than any one human could
A good way to use the current bounty hunter setup without making MP bland
It would be very easy to apply 1V1V1s, and 2V2s (2V2s could allow both players on a team total control over everything, which is/was a separate suggestion on the trello)
If it referenced the bounty.txt, mods would work flawlessly with it
Would make FTL drives actually not totally useless in competitively-built designs
Would make FTL fuel actually important if balanced properly
Cons:
The AI can be very dumb at times
Matches even on a tiny galaxy might take a very long time
Possibly difficult to commentate on/observe, given only one planet can be viewed at a time
FTL jumping might be annoying, because there isn't a good way to balance 'You can jump out of any harm's way" with "Jumping away to retreat is useless". The only way either of these could stop would be by running out of FTL fuel
Only being able to manually control one ship might take feel weird/getting used to
