So I got to work - encounters now are based on a main/bonus pool system. Main encounters are selected from a list of possible encounters (and are finally weighted!) and occasionally bonus encounters that spice up the gameplay a little are thrown in, like anomalies or asteroid showers, etc... The nice part of this is that suns, planets and orbits can now contribute to the pool with their own specific encounters, so a specific type of planet might now have a colony you can invest in and get some passive income from it. Encounters can also be unique so that only one shows up per solar system. The result is a much more varied and balanced experience - neutral hubs are not so rare, some quests are much more difficult to find, etc... Entering a new system is like entering a new dungeon level.
Maybe someday there will be a system for overtaking entire sectors, but those mechanics are a bit beyond me when I'm trying to rush to a release build!
Another feature I've been working on is the ability to load ship schematics. When you capture a ship, not only do you get that ship added to your fleet, but you also have its schematics added to your ship library - which means you can build it at a shipyard. So if you see a design by another player you really like, you can load it and edit it.
Of course, to make it balanced, you won't automatically unlock all the ship's weapon schematics - if you don't have a turret unlocked but the ship you're trying to load does, it won't be added to the ship when loaded.
