Hey, that's not a comment anymore, it's a full review, thank you very much :-D!
For the progression, I always try to show things separately and step-by-step, so the player don't get confused and don't have a lot of text to read. I tried to make the tutorial like a mini-game, with the "T to show the Tips" system.
The slowdown was essential for the experience. When it bugged it was really impossible to aim. I hope it felt like going to quantum space ;-)
The inspiration came after the idea of atoms, but it was exactly Puzzle Bobble, the original. I couldn't implement the bounding aim line like they did (spent hours with raycasts without results...) but I think it works alright without it.
I tried to put a lot of animation and SFX in the UI (and in every input or output). For another game I made (here's the link if you want to try it: https://gotm.io/klustergames/colormaze) I had the critic of not having enough game feel, so I always try to work hard on this now. I'm glad to hear that it worked :-D. And I love menus that explain the core game mechanic, I took for Megaman X as you did! (remember the first one, in the menu megaman shoots a semi-charged bullet to choose!)
I'm sorry I didn't explained well how to open the barriers, I thought that with the tip system it would be clearer. Thanks for persevering and finding out how to play!
Thanks again for your comment!