Features
Other empires will now base their opinion of you on your diplomatic status and how long you've been on good terms, lending significantly less credit to the ambassador you sent to their capital to continuously yell, "GOOD MORNING, FRIENDS! WE, YOUR FRIENDS, THE VISS'ARI ILLUMINATE, FEEL SO FORTUNATE FOR OUR ONGOING FRIENDSHIP! PLEASE PAY NO MIND TO THE 38 ANNIHILATOR-CLASS BATTLESHIPS CURRENTLY POSITIONED BESIDE THE WORMHOLE GENERATOR AT THE EDGE OF THE NEUTRAL ZONE!"
Federations now behave democratically, instead of as some kind of pants-on-head-moronic round robin dictatorship. (No offense meant to the fungoid deinzens of Glabazz VIa, who have always worn pants on their head as a product of their peculiar biology.)
Federation fleets are now jointly funded, reducing the chances that each sitting president will melt down the most advanced capital ships in the galaxy to make mp3 players to avert total, economic collapse.
You can now kick Zorg out of your federation by a majority vote. Fuckin' Zorg, man.
Removed the War Economy policy because most people didn't really understand what it did.
Borders are now open by default, making it possible to actually complete survey quests with more than one step. President MechaTrump of the Dominion of Man vows to overturn this decision immediately.
All of your pops have been put on mood stabilizers, meaning happiness will affect them linearly instead of causing them to bounce between states of neutral, depressed, and elated at arbitrary break points.
All ship weapons have had their range doubled, so they might actually be able to shoot each other a couple times before entering ramming distance.
Oh, shit, we didn't have map modes in at launch? God dammit, who's job was that? Well, shit. Uh, hang on... okay, there we go. Map modes. Damn. That was a bit of an oversight, wasn't it? Man, don't we have egg on our mandibles...
General
Ship combat computers have been renamed. Aggressive computers are now called "Traditional Stellaris Clusterfuck" and Defensive are now called "How Spaceships Would Probably Actually Fight"
Added some new buildings for xenophiles so they'll shut up about being the most underpowered ethos.
The fact that a planet has Natural Beauty doesn't actually make it easier to live there. It just makes lots of people want to live there. Thusly, the modifier has also been renamed "California".
It is no longer possible to avoid ethics divergence by basically not setting up a government on your new colony, letting everyone fend for themselves and go feral, then re-educating them once you have enough manpower for a proper capital complex.
Added Regulated Slavery policy. It's still slavery, but it sounds a bit nicer, doesn't it?
Galactic Ambitions no longer makes a whole bunch of quests become pretty much impossible to complete.
New Wargoals
Give me all your money
Get your smelly, bug-eyed asses off that Gaia world
You suck and you will never amount to anything, loser
Let me in or I'll kick your ass
Stop being a total dick to those primitives you conquered
New - Space Nomads
Space Nomads are actually a thing, and not just Jenkins from engineering making prank calls over the viewscreen with a Halloween mask
New - Diplomatic Incidents
New events that are designed to prevent a situation where every empire you meet becomes your best friend forever
New - Slave Factions
Slave faction has been split into Slaves Who Don't Really Mind Being Slaves and Slaves Who Take Issue With Being Slaves
Emancipation faction is now made of traitors free pops who want to free slaves in your empire
Slave factions now have an effect on gameplay (up from no effect whatsoever)
Balance
Promising officers should no longer appear after literally every battle, filling up your leader pool with mediocre admirals
Energy deficits are now slightly harder to completely ignore in the late game.
Ethics
Non-fanatics have been heavily nerfed for not believing hard enough in their beliefs.
We still have no idea what we're doing with Militarists, so we completely redesigned their bonuses for the second time in two patches.
Fanatic pacifists just can't stay mad at you, man.
Spiritualist is kinda garbage now, and Fanatic Materialist, already the best ethic in the game, has been buffed. Special thanks to /r/atheism for helping us redesign these bonuses.
Modifiers
Youthful Elite no longer implies that you're hiring toddlers to govern entire sectors (though that would explain a lot...)
Components
Laser and Plasma weapons and lances have been nerfed to the point that putting armor on your ships is not just something you do when you're out of power but have some module slots left.
Projectile weapons now deal bonus damage vs sheilds, so the next time you say projectiles counter shields on a forum thread, you won't have some guy go, "Well, TECHNICALLY...."
Fighters have been buffed while point defenses have been nerfed. Welcome to the new, all-carrier meta. Enjoy your stay.
Resources
Some rare resources like Garanthium Ore and Teldar Crystals that you are currently reading about for the first time might actually spawn in your galaxy.
End Game Crisis
Crisis fleets are now no longer able to be countered with moderate ease by fleet-capping with garbage corvettes on like 15 spaceports.
Crises will now happen about 50 years later, allowing more time for your neighbors to build up fleets that they will not use to help save the galaxy.
Unbidden portal can no longer be made to collapse by throwing rocks at it incessantly for a few hours.
Governments
http://i.imgur.com/Vs8M2NI.png
AI
Someone in Twitch chat finally told the AI why they keep getting killed after colonizing Holy Worlds
AI will no longer build robots on planets with unemployed organics. Even if the robots would do a better job and complain less. Just saying. Whirring? No, I don't hear any whirring. I think you're imagining things in your meat-brain. You know, just like the one I have. For imagining.
Fixed a bug where the AI was allowing total wusses into their ground armies.
End Game Crises
AI empires should be less likely to try and wait for the whole Prethoryn thing to blow over.
User Interface
Did you know that some weapons ignore evasion? Oh, we never mentioned that until now? Whoops.
Bugfixes
No longer possible to build a military station in neutral territory and assure the other empire it's just a really elaborate sandwich shop. Yeah, those aren't guns. Those are sandwich launchers. We just really want to make sure you get your sandwiches on time.