The most important thing are the colors. I'm not sure how it works since I could't take a longer look at it but for me it seems like it just picks a random color for each level. That's exactly the thing I was talking about earlier, I was rather confused by what the new color means rather than enjoying the gameplay. Additionally the color was pretty much #0000FF so it wasn't too visible.
You are correct - it picks a random colour for each level. I'm thinking of removing pure blue colours from the list - blue does not seem to gel well with the black background. Each type of bullet should have a different colour - though it may not be the case sometimes. I'm shifting the colour selection to a more deterministic system, so that colour differences are clearer.
I never had a problem with staying at the bottom the whole time, actually I've really enjoyed almost every single pattern's visuals, like really I just sat there and didn't shoot when I could and thought like "Boi that looks awesome!" (except the ones where the arms got crazy - I had other things to cary about then), because one could just be a part of the flow. Now with the bosses jumping around it doesn't look quite as good. This opinion however might easily change when I look more into the game, maybe it'just the beginning.
So far, each boss distributes their difficulty evenly between movement and attack. It's going to change next build so that bosses have their movement/attack preferences - some might move quickly, while others don't move, etc.
Actually, what I just said isn't that important comparing to the fact that the moving bosses affect the gameplay - you cyn't really stay under the enemy if it's going to the bottom, so something should be changed about that. I'd suggest to either let the boss take only the top 33% (or max. 50%) or change the "aiming" behavior when fighting to "just survive long enough" rather than "stay under it the whole time".
I'm considering having a "death timer" - bosses naturally lose some health, so even if you are unable to stay underneath, the boss will die after a certain amount of time (like the TH series).
It feels kinda unfair that the bosses cooperate with Aperture Science while the player does not.
I don't quite get the Portal reference :)
To summerize - I like the ideas, it's just that the implementation should be changed.
I'll try to find some time in the next few days and report how the things change.
Thank you for your feedback! I hope you will be able to enjoy the current build.