I've put down a few games under my belt, all as the Altarians. Here is my initial feedback.
Bugs:
1) Mouse scroll does not work. I have to use arrow keys to move around the map (not sure if this is a bug or just not implemented yet).
2) The planet stats view (right side) does not show the correct statistics for population. It might show 8 when the planet actually has 14.
Music: The initial music is amazing. I love the planet building screen music, it is so epic I find myself singing along with it.
Aggression: So far, the AI seems exceptionally passive. I know you mentioned in your notes that you want us to get out and kill each other, but I'm finding it hard to test the combat systems when the AI basically doesn't want to fight. I recommend a couple of changes just so we can test this out better.
1) Ramp up the AI's aggression AI.
2) Increase the base life support range for ships. Its hard for early warships to get enough range to actually hit enemies (since I can't customize ships yet) so a base increase will let the combat start sooner.
Terrain Improvements:
1) Adjacency System: So far I really like this system. Its intuitive and powerful, its really makes you enjoy planning out your developments. Only thing I noticed that I found odd was the effect on food. For most improvements, the adjacency bonus doubles their impact (10% factor goes to 20%, etc). But with a colonial farm for example it goes from +4 food to +4.1 food....a very small bonus in comparison.
2) Let me set the colony base: Now that position matters so much more now, when a new colony is founded I should be able to immediately place the colony base. Its sickening when you get a new planet, and your colony base is plopped on a big bonus that it cannot use, or is isolated from all the other hexes so its adjacency bonuses are worthless.
3) Tourism is confusing early game: When I'd see a bonus tile that says "+1 to tourism", it took me a while to realize that tourism was a building type I didn't have. I assumed it really meant influence.
4) Base tile bonuses: Personally I think these base tile bonuses are superfulous (aka the +1 wealth for mountainous, +2 research for arid, etc). Between the main bonus tiles and the adjacency bonuses I already have a lot to play with terrain wise. The base tiles I have to click on to see (which is annoying) and graphically they don't make sense (seeing an arid tile over an ocean hex, etc).
But simply put, I don't think they are needed. You could just increase the rate of special tiles if you want more of that. Also I don't need a big bonus to research to want arid tiles...just the fact I can now build more improvements is plenty of incentive to get terraforming techs.
Population:
I'm personally fine with setting up the main economics around population, that seems to make good sense. But considering that it is so important now, I would recommend a guide around population, food, and growth. Right now, there is no real way to understand how this system works unless you are a Gal 2 vet (and honestly I found the Gal 2 system to be fairly unintuitive myself, probably one of the "clunkiest" of your subsystems in an otherwise pretty smooth running game).
I think we need answers to a few big questions:
1) How fast does population grow innately?
2) What impact (if any) does food have on growth and/or maximum population?
Manufacturing: Only note I have here is I find initial production in a new colony to be very low...I find I have to rush to get any reasonable production out of those colonies. A small bump to the manufacturing for the colony base might do the trick.
Starbases:
1) One of the key missing UI notes right now is there is no indicator a starbase has modules to spend.
2) Starbases are one of my favorite things about the Gal Civ series. One thing I have always wanted was a way to increase a starbases impact range. I think this could be a good module, or you could add it as a benefit to the influence modules (which are generally only useful if you are going heavy influence play).
Research:
1) I think that better improvements (aka Xeno factories or Xeno Labs) come along too quickly. It was a criticism I had with Gal Civ 2 as well. Basically by the time I get my improvements going its time to upgrade them all to the next level. What that meant was manufacturing became a big part of any planet just to keep up with all of the upgrades.
Also, with your new systems I don't think it's needed. Between the adjacency bonuses and the bigger connection to population, your wealth/manufacturing/research already tend to scale up with time. This is one area you may utilize your new "era" system on. Basically each era is when I effectively can overhaul my infrastructure to the next phase.
I will say this goes double for powerplants. The fact that I can get a Antimatter powerplant that acts as the equivalent of 10 base factories (plus its adjacent bonuses) pretty early on I believe will ultimately be overpowered. Even if I build just rush buy 1 of them on my main manufacturing planet, I can increase its production rate many fold over.
2) The new specialist tech system is interesting so far. The one thing is I don't see any visual notes that they are in play. For example, when I get the tech to improve my factories manufacturing by 10%, I don't see that noted when I click on my factories.
UI
1) For the planet list (on the right side). It shows progress bars which is great. It would be even better if it could show the remaining number of turns on the far right side.
2) In the terrain building screen, if I hover over the numbers it would be wonderful to see a math breakdown. For example, when I hover over my manufacturing number, I want to see that I have a 10 population multiplied by a 50% bonus from my improvements, etc).
3) When I click on a planet, at the bottom it offers a planet info area. I would love to extend that just a bit, and see a list of the top 3 things I'm building in the queue for that planet.
Overall, I'm impressed by what I see so far. Keep up the good work!