Strange, as I thought the message in Flower was actually subtle enough and didn't bash the player over the head with anything. I wonder where you picked up on the supposed message that cities and (?) public transport were considered bad as there are no actual vehicles in the game to support that. The only "message" I got from this game is the simple statement that industrialization and urbanization are holding nature back and that they are draining the world of its color. In the meantime, there was the mere suggestion of the usage of natural energy sources - windmills - but I got the feeling they were primarily in this game because of their calming aspect and as a way to move the petals. Apart from that, the levels were as open as, say, an area in GTA4 where you get to complete a series of missions before moving onto the next. Of course the scale of this game is a lot smaller - but to me it did not feel that different. Every level represents the dream world (or memory) of the flower sitting in that window serving as the menu of the game and in my opinion, these levels were well-designed and well-balanced.

Regardless, if the game conveyed a stronger message than I picked up on - as you suggest - I do not think this is a bad thing at all. With the constant flow of over-rated games with a more sinister yet equally "crude" violent message, I think game concepts like this are actually needed.