I beat the game!
Well, I have to say: That was added to my list of the most fun and polished indie games I've gotten from this forum, which I hate to admit is a short list. The last boss was pretty fun. Took me a fair number of tries to beat him, but once I figured out the best ways to dodge his moves, I whooped him :D I found that all it took was being patient, completely dodging on some waves and then mostly shooting on others. And the ending was satisfying enough for me.
Also, can't praise the pixel art enough. The atlas, the enemies, the bosses, everything was very polished, fit well together, and basically was of commercial quality. Being somewhat of a pixel junkie myself, I only wish I could make sprites half as good as the ones I've seen in the game. They were very stylish and colorful, in my humble opinion.
Spoiler (highlight to view) --> I had a little issue at the end figuring out where to shoot the last boss on the third form but once I figured out you shoot into the hole where the beam was firing through, I was able to beat his third form quite quickly, and felt that it should have been obvious to me way before I actually figured it out (So I think it was just me, not the game). It would be satisfying to see the planet actually explode from a far off view, flash of supernova style white light and the planet disintigrates.
But it was satisfying to know that Jones finally got to rest in peace. I got the feeling that he was deteriorating throughout the war even though the process of transferring his mind was supposed to be fairly perfected. I also think it's an interesting way to state how war can affect a person's mind long term; and it is pretty cruel to use someone to die over and over again which I think we humans would do if we could figure out how. So the social commentary was great, but not to the point of being intrusive and forced on the player.
Also, after beating the game, I was delighted to see a survival style level to fight waves of enemies in. I didn't even have to ask for one, which is great.
The only real bug I could find was that sometimes the game crashed if I paused it. This was particularly unhelpful when I had to use the bathroom during the last boss XD (Too much information, I know!)
Some of the boss fights were puzzle fights where others were straight up blast the hell out of them, while others were a combination, and I found the balance to work quite nice. I never, ever felt like I was fighting the same enemies twice throughout the game, and I only felt that maybe one level (Force Sector, I think, in the Energy Hive) was a bit too frustrating for me personally, which could be solved by tossing a repair in it near the last 3/4 of the level. I think it's just because the path randomizes a bit so you're learning multiple layouts for the same level. It was the level that took me the most tries, incidentally.
I guess my only couple question are: Are there multiple endings? If so, is it the medals that determine which ending you get? If so, that would enhance replayability. If not, I don't think you necessarily have to do anything differently. (Feel free to PM me the answer if it's major spoilers)
Finally, some advice: If you make any more indie games, which I assume you will (And hope you do!), I recommend charging a "Pay what you will" price, something with a minimum of one or two dollars and a maximum of whatever the person chooses to pay. There are plenty of amazing indie games that charge $5, and I think I would have payed $5 for this game.
I think I would pay $10 if there was some form of multiplayer versus or multiplayer coop. Can't imagine how fun it would be to do these levels with a buddy! Or to shoot him down in a dogfight :D