The flowers are a brilliant idea, more games should have something like them. My only suggestion, add some way that you can put them back the way they were. Passing it turns the flower "off" standing in front and hitting a button turns it back "on"
You copied everything from other games. Almost all the graphics are from Tyrian 2k, some just got different colors. Yeah, Tyrian needed to be re-done, but at least give credit for it.