It's tempting to explain the surprises the game hides in its second half. No footage or screenshots of the game's latter half can be found online, and for good reason. The revelations of the second half of the game are so startling that to know anything about them would ruin the game's impact. (Think of Rez's endgame transformation, and you'll have a good idea as to what Flower becomes.)
Perhaps my reluctance to reveal anything about the game's progression reveals that, in spite of its rather unconventional appearance, Flower ultimately follows a very standard blueprint for storytelling and game design. There is a greater "good" and a greater "evil" -- and the conflict that arises between the two becomes the driving force of a rollercoaster of emotions.