The level layout is quite impressive!
If you die, having to restart the entire intro cutscene is painful (it's very cool to see the first time tho)
Sometimes the start game button doesn't function after you die once.
The scientist guys are a bit bullet spongey, so decreasing their hitpoints or increasing the damage from your guns would help.
For the minigames, having the color flashing puzzle flash more quickly would be appreciated. Also, maybe decrease the length of the code that you need to type