The Odd Life of Timothy Green
(2012)

A couple (Jennifer Garner and Joel Edgerton) is told they can never have children, and are devastated.  They write a list of what their child would have been and bury it in the garden.

That child, Timothy (CJ Adams), appears after a rainstorm, with leaves on his legs.  As the movie progresses, you see the leaves die as various events happen in his life.  After an evening where Timothy saves the town by saving the main source of income, the Pencil Plant, by thinking of a pencil made of leaves instead of wood, they arrive home and he tells them his leaves are gone, and so he needs to leave also.  A loud thunderclap occurs, the lights go out, and Timothy disappears, telling them they have been the best parents ever.

Next scene, the adoption agency is dropping off a little girl for them to adopt, her name is Lillie.
  

Thanks Terri!