The Good
1. Slick UI
The User Interface is intuitive enough. There are plenty of tooltips, which is nice and definitely helps getting into speed. The tutorial hints are also a good idea. The tutorial descriptions are not too big nor too small, just enough to pickup some speed. Maybe the UI could be made more beautiful, and more sci-fi-ish (looks a bit bland now). But, overall good job!
2. Ruins investigation is a good plus
Curiosity and plenty of surprises (mainly good) are a sure formula for a fun eXploration phase. So far I only got positive outcomes from ruins investigation, and I agree that it should be mainly that way. (mostly positive I mean) But, you should feel just a little more afraid/in awe, if possible, when finding one of those ruins. Maybe a specific unit could give better outcome, to make you decide: "shall I go for it now or wait for the "exploration unit"?". First I thought: "only one object texture for every ruin? But then, I don't know how important it would be to add a few more. It's an abstraction after all.
3. Progression overall feels right (so far)
The learning curve is not too high. In the beginning there's a 5-10min overwhelming phase, but it's totally manageable after 30 minutes or so. And, the events assistant, the system that tells you what you have left to do, is nicely done. Gameplay is fluid, and it's easy to keep in control of what can/needs to be done, at least in my first hour of play.
4. Research breakthrough is simple but also quite elegant
The Research mechanic is very straightforward (no explicit tech tree) but it's very simple to pickup also (if you read the descriptions at least). I like that it doesn't tell you everything (like: +20gold) right from the bat. It may feel a bit too simple (or simplistic) to some people though, and while I'm still not fully sure if I like it or not, it is kind of an elegant system indeed. I'll probably detail this point in further posts. Ha, and the sound when you breakthrough a tech is extremely important. I like that a lot. The more dramatic and pleasant the better.
5. Diplomacy is simple but to the point
As the title says, it's very simple. Not flashy, shiny or dynamic (no animations...) but it's very intuitive, and sticks to the point. Still too early to assess the diplomacy mechanic in general, but so far I'm ok with its simplicity. What's important is that the factions have their own personality and that you can have some degree of control on what's going on. It's too soon to tell that though.
The Bad/suggestions
6. Not possible to rename things
It must be possible to rename new units designs in the workshop and cities. I suspect this is in the works though, because the need is so evident.
7. Right-click to cancel and return
Mouse right-click doesn't seem to serve any purpose (yet). Proposed to quickly return from city-screen to map. Possibly re-use this feature to quickly return from Workshop and all other secondary screens to main map.
8. Clicking on menu at the bottom scrolls map incidentally
Menu below (the one with the economy, research, etc) should be made bigger perhaps. The problem is that sometimes I incidentally scrolled the map down when I wanted to access a specific screen. This happened to me more than once.
9. Pathfinding ETA
When movement takes more turns this should be informed to the player. I think this is a should/must have.
10. Unit free move in Workshop
Self explanatory. I felt the need to freely rotate my unit being displayed at the workshop. Currently it keeps spinning. Not good. Takes control out from the player. Player may want to see the new flashy weapon or armor and not wait for the spinning to show it. I think this is important.
11. Map tiles are not the most pretty
Maybe some work could be done graphics-wise in the map. That's where we are most of time and some objects are not that pretty. This is a nice to have thing I suppose though. E.g. Didn't like so much how the alien nests look. They do look repulsive, but aren't they too big perhaps? And the resource tiles seem a bit out of proportion also. Maybe just made a little bit smaller, to fit on a single tile.Oh, and cities are not interesting to look at at all. Don't look that sci-fi-ish, but ordinary cities, and they don't look any special from above (but maybe they evolve with time, I don't know).
12. Music is not bad but not great either
Some songs are nice but others are not that great. And, they should reflect your state perhaps. When you're at peace the game should play more peaceful and relaxed tones while at war the music should sound more aggressive and belligerent. Overall I like some tones but maybe you should look for some extra great songs: couple great war songs and a couple extra-relaxing/non-intrusive sounds. And, sci-fi, sci-fi

The bugs
13. Former in fog of war
My former appeared in the fog of war when built, very far away from my city where I built it.
That's it for now. Remember that these were my first impressions after playing for 1h. But so far I liked the experience, and if I had the time I would probably play more. I feel that you're on the right track.
\Edit: Used version 0.9.2