Personally, I really like the paper trope. In the first 3 games, the decorations were definitely more flat, the environments more blocky, and houses folded open when you entered them. There were also a bunch of paper themed mechanics, especially in TTYD. To me, the paper environments in the new games are only an evolution of that idea.
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(GENERATION 30: The first time you see this, copy it into your sig on any forum and add 1 to the generation. Social experiment.)