That was a lot of pretty neat ideas. You really seem to have paid attention to GMTK. A lot of his advice is evident in this game and it's very well executed.
I think I appreciated the mechanics more from having to figure them out for myself. When I noticed you had posted instructions in the comments, the only rule I had not figured out was grey=ok, black=damage. If it were black=ok, red(possibly with glow)=damage, I may have figured it out myself.
I liked how most the split upgrade tree really had value in upgrading both sides. I thought it would be something like Infamous, were you go all the way with one side and ignore the other, but there really is value in how you split it up. I didn't even think to buy the health upgrade from both the pink and green sides until around my 8th play-through.
Your alternate guns seemed under-powered (from reading their descriptions) so I didn't buy any until about my 17play-through (when I finally beat the game), but I did not expect it to only apply to the color I bought it for. This is a good idea, I just did not expect it.
I will admit the game got a bit repetitive after the 12th play-through, but the desire to see what all the guns did pulled me through. Part of my problem is that every play-through I bought speed and both health upgrades first. Starting a little faster and with 1 more health might have let me decide a better gun or special ability was more important.
Some Notes: Spawning (+$ 50) when I kill something would have been a great help since the game is too intense to look at the money counter while shooting. I liked how you have to modulate your own difficulty by deciding you can survive making the enemies tougher. A texture on the floor would have made it easier for me to tell how fast I am moving when I go straight up or down. Buying both speed upgrades seemed to increase my Y movement more than X.