hi there. I'd like to throw in my own two cents on the music side of the gameplay. Now, I'm no expert, so take it as you will, but I am an avid consumer of any and all music rhythm games.
first off I would personally add more notes. not that it will make the game better but most music games are comprised of a combination of reaction time and pattern recognition. on average games will have 5 or 6, some games will have 8 or more (yeesh but those are a rarity) and some will have as few as a single button or just two. all depends on what's being challenged. Second this popped up most noticeably with the singing bee factory part but it's a big no-no to mix upcoming notes while the player is playing current notes excepting certain cases where the player might look to sing along with the conductor, but the notes need to match or it becomes dischordant. third different speeds of notes are fine, but the last few notes blasted out in the woodcutting song do really need a telegraph beforehand, a sort of wind up sound to "ooooooh I'm a gonna shoot this thing GET READY" if you have the time, I do highly recommend you pick up any of the rhythm heaven games, I believe there is one for the DS, 3DS, and wii. if you can't you can always watch plays of them on youtube to get an idea of what I consider a shining example of what can be done with just one or two inputs. and I believe it's the closest spiritually to your game so far anyway.
*EDIT* I forgot to mention, input callibration timing is incredibly important. I felt a minor lag and while I could get used to it it would wreak havoc on my play as the songs got more complex because I would forget to time my presses ahead of time.