The way you implemented the metroidvania formula withing a rail-shooter is really interesting. I like that despite being on rail you actually have great freedom of movement and you need to figure out where to go and how. But I struggled to locate myself in this world: I wished it had big landmarks in the middle of the loops, so I could quickly recognize where I was and where I was headed. I took a long time to find the way out of the first zone.
My other complaint is the lack of affordance for most of the gameplay elements. I was confused during most of my playtime, having no clue what the different things were or did. I always appreciate a little mystery, but my confusion would often persist after interacting once or twice with an element, which was frustrating. Sometimes it was clear (going through a red circle alerts new enemies, got it) but other times I wasn't sure how cause and consequence related to each other.
Despite the game's repeated warnings, I played with a gamepad because the mouse & keyboard controls were just too complex for me. It was fine, though I would have preferred the acceleration/deceleration to be a boost while you hold the button rather than two buttons you have to constantly juggle between. But it's a pretty minor gripe.
I gave up in the Organic level because the difficulty ramped up too fast for me. I just couldn't shoot down all the enemies while avoiding tripping the reinforcements while also looking around to identify where I was and where I should go (the rails became much longer and twisty between level 1 and 2). That being said, I'm no expert at those kind of games, so take it with a grain of salt.
Again, very interesting entry, with a nice feel to it. I could see it growing on me if I had more time to dedicate to it. Good job! ;)