Maybe not marking the clovers in the museum with a ? but showing a desaturated version would help. That way we could focus on specific missing mutations.
Good game, the whole series actually. One slight annoyance, why not let the player pick up a ball with a click, and use covers/inks with clicks too. That way you wouldn't have to get/find the ball for every single move and drag it.
2nd level is already quite difficult. And in a game that requires precision like this I expect the controls to be more reactive. The double jump often just doesn't fire.
They will become powerful later on if you feed them well. At the beginning just feed them so their growth increases.