Wow, there's a lot of content here!
Your game is very fun to play and progress through. Skill trees are always a great way to help the player feel like they're making progress. That being said, once you complete a skill tree, gaining mutation points isn't super helpful. I wish there was something I could do with my upgrade points once I finished my tree.
I'm not sure how many there are, but I saw three minibosses! Each one felt unique and challenged me in a different way, totally outstanding! To switch between run-and-gun to bullet-hell to run-and-gun between the bosses was super interesting. The Thruster boss was so difficult! I wish I could shoot its missiles out of the air.
The color palette of the game was pretty difficult for me. I had a really hard time seeing enemies, to the point where I'd run into them. Changing the background to be darker would've benefitting this game greatly!
Finally, I was really disappointed at the lack of sound effects. Simply chirps would've turned boosted the tension of this game quite a bit. A hiss of steam when BOB slows down, or a big BOOM when the bosses are destroyed would've added a lot to player feedback and satisfaction.
This is one of the best games I've played so far! Great job!