Tired: the sandbox should start with nations like this.
Wired: the sandbox should give the player options (within reason) with regards to diplomatic statuses with select factions (i.e., empire civil war is not optional due to described events, but the player can set whether other factions are allowed to start at war dynamically).
I understand this may be a lot of dev time that isn't available, but anytime we can see more options in an SP sandbox I think it is almost always the best solution.
EDIT- Alternatively, give Stellaris a go and see if that system tickles your fancy. The games gives you numerous options in tailoring the galaxy and starting factions to the player's tastes. It also gives the player options to ensure their playthroughs are unique in significant ways by altering the AI's starting situations. Something like that could be adapted here, given the dev resources are available.