Some great ideas there.

Another idea could be for players to be able to design their own planets, space stations, craft etc... thus expanding the universe and giving players even more places to visit. The designing could be introduced in the form of tech tree development similar to a realtime RTS, so the player gets to choose the evolution and development of their planet based on the choices they take within their planets eco and tech tree branches.

This way planets could evolve with a lot of unique permutations making each planet unique. This is a danger with games like this having large numbers of planets where each starts to become similar. Giving the player control over the evolution and development of a planet would prevent this from happening.

Maybe each player controlled planet could actually be like a guild hall, but rather than just allowing only guide members to see and use it, all players in the game could visit it's space ports and stations as long as they can get clearance from the guide controlling it. That could be a very cool concept. Whole guides could even be given a star system, so that as they evolve and expand they could move out and colonise each of the planets in their own solar system.

This would be a mixture of SimEarth (for the planet and lifeform development) and RTS tech tree development (for the placement of cities, population development, type of space port/stations that can be built, types of space craft that can be developed and then sold to other players etc).

This could then lead to some EVE style gameplay, with other player guides aligning with each other, joining different solar systems into alliances and federations, to control mining resources and other production, as well as controlling areas of space and systems. Military elements could also be introduced where each player is aligned to a certain home planet, and so with the military from that origin. Being aligned with different solar systems and Military could then get you better missions within those systems.

Equally players could choose to become pirates and sit outside of systems waiting on those travelling alone on cargo runs. Or players could choose to stay independent, running cargo or smuggling illegal items or people between systems.

Player controlled systems could also introduce self policing, when players can choose to become a member of the police force protecting that system, and being aligned with other systems and a certain home world could have the advantage of being able to call for military or external police help if your system came under attack from pirates or opposition systems.