Offer missions to other empires.

I like a lot the idea even if i am not sure your example are very legit or easy to put in the game. Also you can do this things without needing a quest interraction, exept if those things are created only for the quest when a quest is proposed. I am not sure my examples will be better but when i read your idea in first time i imaginated that :

-Each faction can unlock a  fixed amount of written quest via technology tree, or their own quest lines. Each quest can be completed one time.

-When a player unlock a quest, he can add it to his offer in the negociation pannel. When a quest is used in an agreement, the faction that receive it get it in it's quest menu. The faction that offered also in a new tab in the quest menu "offered quest". The faction that offer the quest can cancel it at any moment via the negociation pannel wth the action "cancel quest blablabla".

-The quest take the form of a classic quest for the play who need to fullfil it. It bring lore and it's probably a thing that a faction cannot do by itself, and need help from another faction.

-This kind of quest don't reward only the empire who fullfill the quest, but also the empire that offer the quest at beginning. The empire who fulfil the quest get an unique trait linked to the faction that offered the quest, and the faction that offered the quest initially a unique trait linked to the quest lore.

Examples (just ideas like that, i didnt think about balance or things like that) :

Riftborn's quest : Understanding material world. 

Lore : The riftborn have a lot of trouble to understand the material world from their virtual conception of things. They decide to ask help to another faction to teach them. They need to send scientist and philosophers to an ambassy of this other faction, then be able to communicate and translate the teaching of the other faction.

1. Quest is accepted, a civil ship is created at the riftborn's home system. You can control it and you need to escort it to one of your system with a free pop slot in order to welcome the riftborns scientist and philosophers. This joins your idea "2.) Esscort colony ship to destination."
2. The riftborn ship have landed on your planet. A single pop of Riftborn spawn, and the ship is destroyed (if the quest is cancelled the riftborn pop disappear, if the system is captured by an hostile facion the quest is canceled). You are able to moove this pop via space port if needed. The objective of this part is now to produce  an amount of 250 science and 150 influence on the system with the riftborn pop of the quest, and to build a building called "Riftborn conceptual laboratory" that give no bonus.

Reward : The laboratory is completed and the system create the required amount of science and influence. Both of the two empire get a reward. The Riftborn conceptual laboratory now provide bonus in science and influence, and the riftborn pop on your system give a bonus +10 hapiness. Also, Each Riftborn population of the player who offered the quest now provide also a bonus of +1 hapiness by pop.

Craver's quest : The thrill of the hunt (for bad guys)

The cravers have no respect of other races, but they still have respect for strong hunters. They want to test you, if you succeed to their quest, you will earn some respect (or loose some disrespect ?), and maybe they will also learn from you.

1. Quest is accepted. If you want to organize a hunt, you need two things : hunters and prey. Hunters are easy to find, some of good designed ship may be enough. But preys are not so easy to find without create a diplomatic incident. Good thing, you have a lot of power and create some for yourself. To create those preys, you need to recruit some unaware people. You need to create a building called "strange recruiting office". In those you can sacrify a slot of population and a fair amount of dust to create a fleet of ships on your system called "preys". Those people think they are mercenaries and will go fight cravers on the border.
2. The preys are created. Cravers want to be first class spectator of the hunt, so they want you to lead the preys ships to their home system.
3. The preys are in the place. Cravers love the fact that you bring food and entertainement to their home system. The 3rd part of the quest activate.  Only the player who need to fulfil the quest is able to destroy them. Preys have one turn of immunity when nobody can kill it and moove randomy. You need to kill all the prey fleets to fulfil the quest. That join your idea : "1.) Destroy Ships at system (Pirates or other faction.) This would  also help with ai allies sending help to where you need them to go  instead of them fumbling around your empire"

Reward : The preys are destroyed. The hunt had ended in glory. The cravers are impressed and you hope you will get something from this messy crimes. Your army have learned a lot from this hunt into a hostile territory : you get a special module called "hunter's engine" that give 4 movement speed and a bonus of 5% to damage. Meanwhile, cravers population are now aware that other races are not only whining maggots, their diplomatic negociation cost now 15% less influence.

I have no idea if this is near or not of your original idea. But it's based on your point, I hope. 

My examples were just meant to spark some brain storming. Ultimatly i wanted more interaction between empires beyond trading.  I Really liked your craver quest or just race specific quests in general,however, i thought it would be easier on the devs to set up a bunch of generic missions every empire could offer just to keep it simple. If the devs could incorperate larger scale or race specific quests that would be great! To answer your question your ideas are close to home. Thanks for the input!

Yeah that could be a problem but im sure the talented devs could make it work. The point of this idea is to serve as both instructing you ai allies to allocate fleets in the way you want and to raise diplomatic relations without having to bribe ai empires.  Suprermarioworld Had a great idea to make some quest faction specific whichwould be awesome! Thanks fro the feedback guys!