First I would like to start off by saying thank you for you feedback and criticisms.
As far as the design and balance of the game go, you bring up a lot of very valid points that I had hoped to fix. Unfortunately I ran out of time in the Jam before I could get to really tackling the game's difficulty curve and progression. (I submitted it early due to my sleeping schedule being poorly coordinated with the Jam such that the last 10 hours I would be either to tired to work or actively sleeping. Thus I wanted to get it in early to avoid missing the deadline). I will defiantly continue to work on the game to get in some of the features I missed, optimize the code, and balance it out so it really is possible to achieve the highest rank in the game.
As for the theme... yes... that is entirely what I was going for and don't let anyone tell you any differently!
But in all honesty I hadn't even thought of that, in truth as I was developing I realized I wasn't doing enough to really sell the idea that you were fighting machines which is what led me to implementing the hacking mechanic. (Though even with it the Hacking mechanic if anything pushed the game closer to a hacking themed shoot em up in space than a war against machines.) I also tried to to really sell the idea in the lore through the In-game manual, but ultimately, I think my delivery on the theme was very weak and you are basically only fighting machines on "paper" because the lore text said so.