Hi Stardock people: I played a game on the first alpha. You promised we wouldn't have fun, but I did. The game is beautiful. It's in an excellent shape for an alpha. I have spent many enjoyable hours playing GC2, and expect the same to be true of this. While I was playing I gathered some notes and observations. I hope my feedback is useful. It is of course mostly criticism, but don't mistake me for being disappointed; I'm not.
I can hardly expect anyone to read any of this, let alone all of this, but if you read anything please read my one BIGGEST ITEM™ before I distract with small details: There seems to be no production and research overflow. With no production and research overflow, about 75% of my time in game is spent microing planetary spending, to avoid waste. (It's either that or accept what amounts to a 10-20% tax overall on my manufacturing and research productivity.) That's not fun. The game would be a lot more enjoyable if it just had overflow, so I didn't feel like I had to do that. 
Anyway, moving on though my game was played on the first alpha, I tried to confirm that these are all still issues on the more recent version. I didn't really pay much attention to quality and challenge of gameplay as such, since I would expect the AI to have minimal attention until you nail down the game mechanics. Anyway, below is my wall of text, loosely categorized...
Title and Main Screen
The first thing one sees when starting up GalCiv3 is Lord Kona's face. It's a credit to your artist that he was able to create such a genuinely creepy creature, and I wouldn't change one thing about him given that he is Lord Kona, genocidal despot extraordinaire, but I might prefer something a bit less unsettling than having him staring deep into my eyes as the intro?
The main menu screen pleasantly reminds me of the original Civ4 opening menu screen.
Setting antialias shows the message about needing to restart to see the effect, but changing interface size does not produce a similar message, even though it apparently requires a game restart.
I hope the ship animation speed is adjustable, or at least ships with a slightly faster default.
I still love the writing. "No matter how many slaves we have, it seems that autofactories can build things faster. We'll just have to find a more delicious use for them."
"I feel no need to choose planets to colonize based on whether local food sources have ideas of their own about who owns the place." I am delighted to see the flavor text was written with such evident gleeful delight, though there's of course more to do till it's up to GalCiv2's standards.
Saved games appear to be sorted alphabetically? Most recent first may be more intuitive.
The workings of the economy seem far, far more clear than in GC2. I think in one hour I understand GC3s economy rather better than I do even after years of GC2. 
Edge scrolling is not active yet apparently.
It would be nice if tabbing through ships executed those with pending moves, so you're not wasting turns on ships that finish their moves and have more moves remaining, before the turn ends. (FE had roughly the same issue.)
Pathfinding estimates are off, and seem to consistently underestimate the amount of time it takes, even in very simple cases. Consider this leg of a multi-turn move. A constructor with 6 moves, it's marked at arriving at a certain hex, but that hex is 7 away. To repro easily: take any ship with 0 moves left, then click various far away places, note that the first turn move has one "extra" square it should not. (Again, it seems like FE had roughly the same issue.
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The Altarian's system has two Pos (you are not po in Pos). Easiest way to see this is to start a game with the Altarians and look at their planets.
Texturing on some planets along the side edges might benefit from some attention.
That weapons and invasion are less prohibitively expensive in early game is a great improvement. With luck, maybe farmer's gambit colony rush is no longer the one right strategy. 
My game consistently crashed beyond a certain point so I stopped playing. It appears to be playable again in the second alpha, so I may continue; I hadn't yet gotten to combat yet. 
Starbases
When you send a fleet of two constructors at a starbase, one seems to be absorbed and available as a module, the other joins the "defenders" of the starbase. I might expect the starbase to "absorb" both? Or, do something other than treat them inconsistently?
It might be nice if there is a visible cue about whether a starbase has available modules, or defenders, similar to the little icons there are with planets.
The tooltip "starbase effect" seems more distracting than helpful. Pic
Planetary Level Stuff
On the planet layout screen, GC2, a usable tile was more obvious because there was a strong visual hint. It's not as obvious with the straight hexagons, at least to my eyes. Something akin to the little "edge dimples" in GC2 would make it more clear. E.g., in the following pictures I spend less cognitive effort figuring out what usable GalCiv2 squares were, vs GalCiv3 hexes.
Positional bonuses are nice, but since building position is so important, it seems like we should be given an opportunity to place our colonial capitals as well? Especially when the game seems to think planting a colonial capital on a tile with a bonus is A-ok? 
I got the same "morality check" for every planet I settled, to join people with pods for a research bonus. I was a very malevolent person.
But maybe some variety on the choices may be nice.
I built a slave camp in Nunavut. Yet, it seemed, as you can see, not to be there -- it seemed to be having an effect, I think, it just wasn't there. How can I keep an eye on my slaves to ensure they are living an empty life of drudge and toil, if they are invisible? Impossible, I say!
The infocards on planets seem to have strange inconsistencies sometimes. Consider, the three infocards (these are taken from the same screenshot, just re-organized), the one in the right sidebar, the one in the hovering tooltip, and the one in the bottom-left "selected" infocard. The money indicator is (1) off, and the icons in the display are kind of wacky.
Notice in the above it claims earth has 12 tiles. I manually count the tiles, I find there are actually 11 used/available tiles. See here. (I am counting my invisible slave camp.) Overestimation by one of actual tiles seemed to be common.
Here is another example here we see disagreement on whether earth has 11 or 12 tiles this time in the main interface.
Production Possibilities Frontier Graph
Though less efficient from a UI perspective, I always like when games with "three axis" spending let us set the point at the 3D production possibilities frontier on a 2D interface, as you have done here. It's less efficient in that it technically provides no more information than two sliders would (a la civ 4 or galciv 2) but I find it more visually engaging and intuitive -- please don't go back to sliders.
That said, I'm not sure why it's a circle? GalCiv3's production allocation has no notion of decreasing marginal benefit, so it seems like a triangle would have been a more intuitive choice? (And if you did have decreasing marginal benefit, the more natural choice would be something resembling a Reuleaux triangle, not a circle?)
Do the inscribed Reuleaux triangle and the three lines converging in the PPF represent anything? The three lines I'd be tempted to think of as axes, but then that's where the circle confuses me.
Take a look at the PPF graph, the term "manufacturing" here seems to mean two things. First (on top) in "adjust manufacturing spending" it seems to mean spending among all three categories. Second (on bottom) in "production" it seems to mean spending towards making buildings and ships. Possibly avoiding the overloading of two terms would be appropriate here.
Nothing visually connects the colorful PPF to the "production" table under it, even though they're displaying intimately related information. It seems like it would be simpler, and more clear, if those little numbers simply appeared next to the icons in the PPF table. Alternately the icons in the "production" table could be same as the icons next to the PPF, if you really wanted this second table for some reason.
The tooltip displaying the proportions of spending is a bit too narrow to display 100% without wrapping, wealth is the wrong color (yellow here, should be green for consistency with the curve?). See here. Things are definitely better than in the old alpha version though (that one had character level wrapping).
I might like this PPF interface available without having to visit a separate window.
If you "govern planet" then change production levels, times to completion are not updated till you do something like drag the queue around, add another item to build, etc. It would be nice if the build times adjusted as we drag in the PPF graph, just the numbers in the left-hand-side "planetary statistics" are modified.
I like the colorful PPF interface, but I wonder how it is perceived by colorblind people?
Building Stuff
The single production queue is a great move, that simultaneously removes unneeded complexity, while increasing the depth of the game by presenting the user with an interesting non-obvious choice.
I'm diving a bit more into upgrade costs. A xeno factory costs 48 production, basic factory 20 -- costs of upgrades are not explicit, but by fooling around with various PPF settings, it looks like upgrading from basic to xeno takes 23.8. Research lab costs 18, xeno lab 40, upgrading costs somewhere from 19.1-19.8. It seems odd that building an obsolete structure then retrofitting it into a modern one, costs less than just building the modern structure?
Should superiority society be an upgrade from annexation guild? It currently is not.
When building planetary improvements, the cost is listed. When building ships, it is not.
Edit: Whoops, sorry about the broken first image link, should be fixed now.