Just a quick suggestion: moving the respawn point for the Lab Boss fight to the room adjacent to it. It is kinda annoying to have to start all the way back at the beginning of the mine everytime you die.
Also the ball seems to sometimes fall right through the paddle when you start a new life. I don't know if this is because the ball falls down first, then bounces off the paddle by default so if the paddle isn't there (ie because you are running around because you are up to your armpits in ninjas and blobs) it just falls straight down.
It would be nice if the camera was pulled out more and locked for this fight because so you could always see the full TV screen. This fight can get very very hectic very very quickly because of everything you have to juggle during this fight. Not that it is a bad thing. I actually like how it adds a layer of planning to the fight. Oh yeah, this fight is probably the best argument for being able to move and shoot at the same time
It is a pretty neat fight so far (haven't beaten it yet; took me a while to figure out WTF I was supposed to do

).
Do you plan on releasing the soundtrack in MP3 format at all? There are some pretty excellent tunes in there that would be enjoyable to listen to outside of the game. EDIT: Just beat the game. Give my regards to Yesso for the tunes!