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.
At E3, thatgamecompany's Jenova Chen explained Flower as an experiment to evoke emotions that games rarely, if ever, touch. Serenity moves to excitement to intrigue. It's unsurprising that a game named Flower can evoke such feelings of relaxation. However, later levels introduce new gameplay mechanics and artistic elements to drastically change the mood. The second level is incredibly empowering, giving players control over color in the world. The third level introduces wind, forcing players to rush at incredible speeds. When players go down a rocky canyon, the feeling of serenity is long gone, replaced with something much more thrilling.
Flower becomes even more daring, delving into the feelings of powerlessness, fear, and ultimately, triumph. The gameplay evolves into something more than simply collecting flowers. Somehow, Flower is able to perfectly mesh the "story" and the gameplay into a completely inseparable whole. This is certainly an experience that could not be recreated in any other traditional storytelling medium.
Those that believe Flower to be nothing more than casual junk will be doing a great disservice to themselves. There is a "point" to the experience, and it ultimately is a "game." Casual and hardcore gamers will find different things to appreciate about Flower -- and no matter what your gaming taste, Flower will tug at your soul. That is, provided you have one.