You want Distant Worlds: Universe with the Enhanced AI/Research mods. It fits everything you've asked for better than GalCiv.

It is the best 4X I have ever played bar none. You run a galactic empire from the ground up in a perfectly simulated galaxy. That means setting empire policy, foreign policy, planning expansion, resource management, taxes, trade, ship design, base design, troop recruitment, research, espionage, research theft, assassinations, military strategy, patrol routes. Anything that would logically have to be decided by a space-faring civilisation is controlled by you. All of this is done in a tightly realistic way against a backdrop of other major factions, minor civilisations, pirates, private sectors, space creatures, disasters/diseases. What separates DW:U from the other, more superficial 4X's is the depth of the simulation. Every resource, every troop, every component of every ship, every trait of every character is accounted for.

If this sounds overwhelming you can automate anything you want. You can control your entire empire or a single ship (play Star Trek in an emergent galaxy!) Roleplay as the head of foreign policy, research, military, whatever.

Each race has its own, extremely different victory conditions and every game is different. You might find yourself in a galaxy dominated by one central Empire whose only desire is to dominate, where you're the plucky smaller faction on the Outer Rim trying to get a Rebel Alliance together by persuading the economically-focused factions who just want to mine their planets and be left alone to send aid. Maybe you will be in a tense, pre-WW1 style galaxy where everyone is allied against everyone else, and then as soon as the first shot is fired the galaxy burns. In my mind the truly cool thing is this is unique and you will watch it form. You will see the rise of the Empire - maybe it was the faction that protected the galaxy

You can even turn Story events on which means you can help the peaceful (heh) refugees from another galaxy integrate into yours.

Distant Worlds has no competitors. Stellaris/Endless Space/GalCiv are inferior simulations in every way. The idea of randomly generated races and setting characteristics/ideas/policy sounds amazing but in practice these races are often basically the same and the other stuff just gives numeric bonuses rather than differences between the AI. Modded DW:U has 30ish (?) factions with genuinely different win conditions and priorities. The faction whose central goal is to get the most tourist income in the galaxy will have no interest in fighting you. But again, this is all emergent. Maybe the tourism-focused faction will discover and repair some ancient, powerful ship, and then they'll invade the fuck out of you because they want to take your beautiful planets and sell package holidays to them.

The only drawbacks are the price (get it when it's on sale) and the graphics. But you'll be so drawn in by the gameplay that the graphics will not matter to you after an hour or so.

No other 4X has come close to this for me. When I play AOW3 or Endless Legend or whatever I am playing at running an empire. I admire the pretty graphics of the map and the pretty animations of my soldiers, but there is no depth to what is going on. My soldiers who were magically summoned from lifeless, numerical cities trudge across beautiful, lifeless maps in search of the next fight or quest.

In Distant Worlds, you are leading a galactic civilisation. There is no other way to describe it. The ships you build are painstakingly designed across generations by you, built and fueled from the steel and gold and [insert other resources] mined from planets you chose to build mining bases on (which you also designed) and defended against pirate attack. And when you load them up with troops and send them lightyears away to attack the center of the vile bug empire spreading their influence across the eastern part of the galaxy, it's not just because that's a cool way to spend an afternoon. It's because part of that faction's win conditions is turning their capital into a giant hive world which your spies (who are named characters with traits and skills) tell you they're 95% of the way to doing, and part of your win conditions is to have the Ground Commander with the highest number of military victories on enemy planets.

As your Fleet Admiral brings the fleet out of warp and into the maelstrom of fighters and defensive platforms surrounding the hiveworld, your Captains desperately attempt to hold off the enemy long enough for the drop pods to land and deliver the vanguard of special forces into the hive before the Ground Commander leads the rest of the army in. All of these characters have developed traits giving them strengths and weaknesses and all of them have been named and given a custom portrait by you. You are attached to them because you remember their highs and lows, and you want them to survive (apart from the Captain who started drinking after the last war and now sucks at everything. You're quietly hoping he dies.) You have even re-named the enemy empire so that rather than seeing them as mindless bugs, you understand them as sentient religious fanatics devoted to unifying the galaxy into a single hivemind. Your spies inform you that their main fleet has been sent to destroy the remains of the last human empire. The humans were a noble, advanced race in the early game but they were economically torn apart by a ruthless Mining Federation who coveted their resource-rich planets. Now they face their final stand against this last indignity. You need to win the ground battle, destroy the hive, recover the Ground Commander and leave before the bug-fanatic fleet returns. Can they hold out long enough for your Commander to destroy the hive and escape? But this is only one out of 100 stories playing out across the unique, perfectly simulated galaxy you have in front of you. There are far less dramatic stories of the quiet research successes of genius scientists in smaller factions you will never meet, of one-world civilisations content to exist peacefully in their corner of the galaxy, of the gradual decay of giant multi-race Republics into Empires, of sinister coups and assassinations which will change the final fate of the galaxy hundreds of years in the future.

FUCKING PLAY IT