Excellent. Almost commercially viable, and one of my favorite things I've seen on Newgrounds thus far.
The story was engaging and well put-together, and combined with the upgrade system to make this feel more like an atypical action RPG than your standard space shooter. It kind of reminded me of Transcendence in that regard. The graphics had considerable nostalgia appeal and were reminiscent of some of the better titles on the NES. The difficulty seemed appropriately paced. Some of the missions were excessively difficult at the time I undertook them, but this is probably because I visited locations in an unusual order and did not choose upgrades properly. However, by the end of the game, I was able to blow through everything with ease. One possible improvement might be to add a difficulty rating to each map zone, not just each mission, so players will have a better idea what locations are suitable for their current upgrade level.
The only real complaints I had were with a couple of endgame bugs. I don't know if this was supposed to have a "new game +" feature, but after attempting to restart the game at the end, I got to play through the intro again with all my credits and upgrades, and then was dumped into a universe with nothing left for me to do. Going to the people's council resulted in a bugged-out mission select screen with no text. The game still said there were two missions available in the Nyx Conglomeration, but none of the locations there were active. I searched thoroughly for hidden hotspots; but if there were any secrets there, they were beyond my ability to find. (I didn't find any of the secret medals either.)
All in all, I just wish it were longer.