I hope its a feature

And I do think it isn't necessarily unbalancing. You need to research two more techs beyond Xeno Ethics to get to it, and it is an expensive building. On small maps with few planets, the time and cost to get it barely pays off (I once rushed to get it and watched my 118 taxes per turn double to 236, and then my entire economy crashed). There is still a balance to using it.

On larger galaxies, you always want it. But it is the biggest reason why Evil is the best long term choice.

Technically, the MCC is a bug. You can look at the PlanetImprovements.xml file and see the missing "bonus type" XML flag for yourself. But it's a bug that's arguably more interesting than the feature that was supposed to be in its place, so I can understand why it hasn't been a priority to fix.

I agree that it makes more sense for Good to have the best economic long game, though. Just giving Good something like a +100% Economy building and taking it away from Evil would go a long way to repairing the strategic imbalance between the alignments.

OH, yeah! I like that. Evil still gets artificial slave center, but you are taking all of those penalties with good ethical choices because you know a juicy +100% economy waits for you down the road. Great idea man!

You would have to change it's name...Good shouldn't have a Mind Control Center!

Giving Evil new weaponry is perfect in line with the aggressive and destructive path though.

It is enjoyable to play all three alignments, though I personally like playing good the most. I have always wondered why SD has consistently made good the "ugly stepsister" of the game, since any discussion I have seen (such as this thread) ranks it a solid third and a serious disadvantage to play. Does the development team believe that the three alignments are balanced (maybe we are not seeing something?), or is it unbalanced on purpose?

Shouldn't the loyalty and morale/approval bonuses, for good and neutral respectively, be swapped? I mean, wouldn't it sound a little better? And it'd balance things out a bit. The 5 colony maintenance bonus, hmm, isn't it like handing you 60bc for free? Once you have 5 planets I mean. Sounds a little lame.

I wonder if capturing the civ capital was just a fluke? The Drengin declared war on me and had 17 worlds. I was rated #1 on the CNN and went for the quisk assualt on their civ capital. After destroying their fleet (around 30 precursor corvettes) I invaded and captured their capital. The next turn they surrendered. How did they get 30 ships in their capital? Did they move them in each turn to replace losses? Maybe my graphics was just to fast for me to see(Asus 8800 GTX)? They did have some fleets within the sector just setting around and seemingly not being used. I like playing good, but evil races get all the permanent bonuses. Right now I'm playing Altarian in my game and I chose all the evil permanent civ increases, and good for all the money choices. I never got considered an evil race. But I got to keep all my evil bonuses when I made my ethical choice for good.

Yes, you do get to keep the benefits (or penalties) of your choices. That is why you may have to pay BC's to choose an alignment other than they way your choices have defined you. Choosing some good and some evil can balance out so you remain aligned where you started...

Good not so underated as you may think, you have to be smart in the way you play them. For example when I make my ecoamy worlds (usally PQ 20+) I ramp the population cap (to around 20-62bn) to be one of my most poplated colonies because when you research consepts of right the mantianance costs of your 12 most poplated colonies is waved. The defences come in very handy in the middle of the game when good starts ganging up on evil. I just give them all the defencive techs and we (ME, Darth, Alrains, Torians) Chop off the evil civs one-by-one. But your right in saying that good gets a raw deal.   

Possable improvments may include:
The ability to entrench worlds and form riesistances after occupation by enemies.

Anything on my running ideas thread: https://forums.galciv2.com/?forumid=247&aid=150178#1188775

I forget what its called but with evil you also get that building that gives your military a boost. I haven't tryed to see what the actual difference is but i reduced military spending to 10% (trying to tech-up to make my next invasion fleet). and im putting out a constuctor on just about every plantet in 2 turns. No one really talks about this building. Ill see the effects better when i start making real ships.

Then you get free invasion tactics and free starbase upgrades. The 100% economy boost is great, got me out of the red and into the green big time. Its ok that you seem to not be able to flip planets, i cant seem to get that done anyway.

Every time those choices come up choosing good means taking a hit immediately, and then a hit later in the "powers" that good gets. This should not be the case because it makes for a bad story.

The game should be more dynamic and less predictable.

For example, you land on a planet and find a primitive race. You take some kind of hit for leaving them alone and not enslaving them. A few turns later you get a positive event where you find that the primitive race has an ability to commune with some precursor tech that gives you some kind of tech bonus.
The chances to receive a positive event should increase with the more “good” choices you make. Likewise the chances of a negative event should increase as you make “evil” choices. This makes things feel more real and that are choices have more unforeseen consequences.
Oh and evil should not get along with evil for by definition evil is self seeking.
Evil should get a manufacturing bonus not an economy bonus. (slave labor, but lack of creativity)
Good should get an influence bonus (economy because of tourism). Good should have a diplomatic bonus against all alignments. (better to flip planets that are within your influence)

Good choice for neutral to get the tech bonus

To sum up
Evil: manufacturing, weapons, (military conquest)sacrifice people to use like money
Neutral: science/moral/trade (science vicroty) : more money from trade
Good: Influence/diplomacy (for a diplomatic/influence victory): more money from tourism
More random events based on your choices that make the game breath more.

So when do you get the benefits from evil on the tech tree. I am mostly interested in the +100% econ, and 50% military production. Do you get either of those when you research xeno ethics?

Personally, I think it might be worth examining the possibility of having an alignment-based base morale setting for population, if they're going to go along the strength for conquest on the Evil side and strength for development and diplomacy on the Good side.

Let's look at this from the point of view of the people being cattle and the government being altruistic, malevolent, or orderly. In a malevolent government, the government cares little for the people, so has to spend more time and resources policing its people. The more the people, the more intrusion, the more difficulty in keeping the peace. Have too large a population and they'll either become unruly, being all serfs, or require immense resources to manage.

On the other hand, you've got a goody-two-shoes government that's interested in benefit for the people, altruism, and general public well-being. Who wouldn't want to live in a society where the lowest of people are treated fairly, opportunity is available to all peoples regardless of birth, and all that good, Utopian rot? Masses of people would love to be part of that sort of society implicitly.

As a result, of course, that would mean Good would have higher manageable populations, more economy, more influence, and a larger number of troops to defend their planets.

Hit the nail on the head.