Pixeljunk Shooter is longer, Flower is overall better as long as you "get it" but if you don't you'll probably hate it and think it's stupid (see Hatmoza)
Here's a good qualifier: If you just want some really fun gameplay and like seeing physics interace than Shooter is the way to go, but if you're someone who appreciates storyline and a sense of atmosphere and art then Flower is simply beautiful.
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