Ok, I've spent some time playing the game and the following are my thoughts. Keep in mind I'm not an authority on games and my opinion is simply that of a regular forum goer and of someone who plays perhaps a few too many games.
I'll go over the places where I think you can improve.
Firstly, I think the Instructions screen needs to be more than simply the controls for the game. A kind of 'How to Play' would be helpful since your game is a mashup of several genres and confused me a little bit initially. If there is a sort of written tutorial, I wasn't able to find it. The first few times I played I found it a little difficult to learn while being attacked and I felt a bit over-whelmed. I re-started on easy, which made the learning curve less punishing however it certainly made it a little frustrating to lose without really knowing how to better improve on what I'd done. I think a lot of people who would actually like the game might be put off by that initial 'trial by fire'.
The next thing that needs mentioning is the menu pop-up system. It gets in the way a fair bit frankly, and detracts from the game. I'd prefer a static toolbar-style menu if it prevented the game play area from being cluttered. A few times while playing I was trying to hide the menus and they didn't close - the Research screen in particular, seemed to not want to hide while researching - which made actually participating in combat a little frustrating. The transparent nature of the menus means that don't hamper combat, they just get in the way however it detracts from the game overall.
Another issue is the pace of the game, at least initially. I understand the style of the gameplay, however there were moments where I was simply watching the energy and metal counters tick up so that I could build/research the next item I wanted and it was a tad boring. Again, I understand that this is a necessary evil, however I think that at its current pact it simply drags the game out rather than facilitate any particular aspect of the gameplay. I'm not really sure how best to do this, but I would perhaps grant a larger starting amount to speed up the opening moments of the game.
The next thing worth mentioning are the visuals. As Burningpet has provided ship graphics (and they look great, btw) and already made a mockup of a different set of menu graphics I won't cover this in too much detail, however its certainly something that will elevate the game. I don't mean the sprites or such, I basically mean the visual identity of the game - the style. It lacks a little bit of a cohesive nature. It doesn't feel like a 'Fangorodrim' visual style so much as simply having visuals.
The last item I'd like to mention is the controls for the game. The tank (turn, then move) style controls made combat a bit of a chore and feel a little at odds with the style of the game. I'd much prefer the press up to move up, press left to move left style control system as it would make combat a bit more fun, albeit a little more arcade in nature. If this slower nature is intended you can ignore this part, however with an avatar-shooter mixed with strategic elements, the avatar-shooter kind of gets a bit more of the focus in term of minute to minute gameplay and unfortunately doesn't carry the weight of the minute-to-minute gameplay well enough. This is entirely my personal preference, however.
Now, for the points which I think you've nailed.
Firstly, and the major point I want to point out from my entire post, is I think the concept of the game is interesting, fresh and fun! It has a huge amount of potential, and I think you've got the makings of a really great game here. The idea of 'Sins' meets something like 'Asteroids' is pretty original and you've nailed it pretty well! It's simple enough that its easy to get the hang of and yet complex enough that it has depth, and warrants replaying a few times. I like the mix avatar-based combat with strategy-based combat and 'empire' management. Once refined via the above points, I think you'll have something pretty damn good that alot of people will enjoy! In terms of the overall gameplay and its mechanics, I can't think of any real way to improve - which is something you should be proud of.
The implementation of the game in terms of the program itself is also pretty damn solid. The base building, researching, etc., all just works. No crashes or bugs that I was able to find, minus the ones I mention below, and it just worked out of the zip file. A problem for some Indie Games is that they require a bit of tinkering to get working or running as intended. Good job there!
The balance in terms of damage, cost, etc., works very well. As with all games you eventually reach a point where you have enough resources to spam a little, however thats the snow ball nature of static resource gain in a game with expandable territory. The only real complaint I have is that the start of the game feels a tad too slugish and it detracts from the overall experience somewhat.
I noticed two things that I thought worth mentioning. The first is a glitch, I think. When your ship has been destroyed the game seems to slip into slow motion? However, if you click outside of the window of the game and onto your desktop, the game runs at normal speeds. I'm not entirely sure if this is intended. The last thing I want to mention is that the text is a little blocky and hard to read on my primary monitor (1360x768) and secondary monitor (1440x900). It might be the resolutions that I use, however it did detract from the game.
Overall, I think you have a good game that, with refinement, will be a great one. Good work!