Let's face it, at the moment alliances are sort of crap. They work as a sort of protection from war and a victory condition, but nothing else. In Galciv II they had both advantages (you don't need to fight alone) and disadvantages (you will need to fight wars for others) and it made sense and all that good stuff.
This is how alliances work currently:
-Allied factions never declare war on one another. Uncertain, but I believe one certain mega event may make them declare war regardless.
-Victory condition (depending on map/game settings).
-Some factions dislikes an alliance containing factions with other ideologies, making it harder for them to join.
-Allied nations may get angry (and even leave alliance) if you declare war or is declared war upon by one of their trading partners
-AI never form alliances ever.
This is how they should work:
-Allied factions never declare war on one another. Aforementioned mega event has no effect on allies.
-Victory condition (depending on map/game settings).
-Some factions dislikes an alliance containing factions with other ideologies, making it harder for them to join.
-AI form alliances if their ideologies and relations are great, especially if there is a greater threat.
-Allies always help one another, failure to comply will break the alliance.
-If the player got two allies and these two are at war with eachother, they will not demand help from the player but will give him/her a word that it would be appreciated (with bribes).
-Declaring war on an ally will have reprecussions, as you will come off as a backstabber.
I hope that something is done about this. I often cheat just to imitate the effect of real allies once I have made allies in-game, removing enemy shipyards and stations to simulate a pretend fleet. It's pretty silly. I also remove everything my allies own because they are being unrepentant asses. Then I name their homeworld Poop before I invade it.