So, in order to communicate with one another, you'd need to research the "universal translator" tech, which would allow for communication.
For you to be able to have an alliance with another empire, you'd need to have a certain time of peace with that empire and be of relative equal size (number of planets colonized (outposts not counted)), otherwise you'd just be assimilated in the empire.
You could be able to share stockpile access, research points, specific technologies, supply and sensor vision. For an alliance to be possible you'd need to share at least three of these.
Technologies provided by the diplomacy tree would be:
- Empire boundaries (systems with a thick supply connection
- Universal translator (allows formal communication in game (chat is informal));
- Universal translator 2 (makes the penalty of having different species in the empire lower);
- Trade (allows to share stockpile and supply access, depends on universal translator);
- Research agreement (allows to share research points, depends on universal translator);
- Shared technology (allows to share researched technologies, depends on universal translator);
- Interstellar data stream (allows to share sensors);
- Interstellar negotiations (allows for the techs below, depends on universal translator);
- Declaration of war (allows sending of a formal declaration of war, which ends all treaties and lowers the happiness penalties of combat, depends on universal translator);
- Peace treaties (obvious, depends on interstellar negotiations);
- Trade agreement (increase production of both empires involved in the trade agreement, depends on interstellar negotiations);
- Prisoners of war (allows for the diplomatic option to give back all prisoners of war, increasing the happiness in the other empire, depends on interstellar negotiations);
- Alliances (obvious, depends on interstellar negotiations, allows for galactic unification project (when completed it is a victory for the empire who builds it if the empire has an alliance with at least 2/3 of all other empires).
When one empire signs a treaty with another empire, the treaty could affect the happiness of its citizens. This happiness change could differ per system. Things like the treaty type, how your populace considers the other species, proximity to the other empire, whether the other empire contains the same species, whether previous treaties were honored. Things like that.
There could also be a mechanic which marks certain planets as a core world of the empire after a certain amount of turns. If such a planet (or system) falls, the empire would have a reason to go to war with the occupying empire and citizens on that planet/system will be less happy. The "core world" mark would be lost after 50 turns of not controlling the planet, upon which the empire currently controlling it starts building up core value on the planet.
When an empire goes to war in violation of a treaty, it loses happiness. However, if he starts the war when the other empire is occupying his core worlds, the happiness penalty is lowered.
Also, combat could come with happiness penalties. Especially ground combat (imagine troops coming home in body bags or not at all). This has the effect that conquest of other empires becomes difficult. If you're dealing with large empires you're at war with, than it might be a prudent idea to start peace negotiations before the attacking empire's worlds (and perhaps even fleets) start revolting.