Wow, this game really surprised me! All the systems work really well. I really liked the upgrade system, the Ancient Tree boss, and the secret room that appears where you can upgrade between cycles.
I think the only things I missed were maybe a few more animations and environments that make it easier to identify where you are entering in the level, like the dojo and other areas.
Also, the SFX for the Ancient Tree's bomb attack is much louder than the rest of the game's sounds, so it could be balanced a little.
Great background music! Overall, really nice work.