Settling a new system feels a bit shallow, as the only thing that you do is sending a fleet there, then waiting, while other factions have no convenient way of taking it before you finish colonizing. What I would suggest is adding a way for the other factions to contest the colony if they wish to, before it finishes.


 It could be done in a way that if for example a faction lands a colonizer probe in a system, other factions could also go there and and contest for it, then it would bring the colony in a "contested" state where both factions have to put resources into it which can be industrial power, influence, dust or whatever, and at the end the faction that put most resources into it takes the colony. This would cause a bit more border friction between factions without actual war, and it would add a new way to compete against other factions aswell. Factions should even be able to do this against their allies, since it involves no combat.


 In addition to this there could be a new option on the diplomacy screen to threaten or pay the other faction to step back from the desired system. Or it could perhaps even be possible to send pirates to kill off the supply fleets sending the supplies to the contested system.

 I believe this system could increase the flexibility of the game because factions would get an extra way to stop others from expanding, even their allies. It would also make games on harder difficulties harder, since the AI has a resource cheat, so they'd be able to compete against the player more effectively in this matter.