I really like this idea. The visual feedback for the boxes breaking was really helpful for me to learn the different uses for the modes in the game. The presentation is also really cute!
I also noticed your comment below about adding sound, I like to use JSFXR or SFXR to add free sounds quickly to my games. It's a really easy tool for sound effects if you don't have much time so it's worth checking out if you're interested :)
Anyway I really enjoyed your game, the modes add a good variety to the gameplay and solving little Metroidvania puzzles is a super engaging take on the theme. Great work :)