The impression I got from the graphics changes is that maybe it's an attempt to make it more accessible? The darker look might be easier on people's eyes, and the blue borders might stand out against the warm palette more? Maybe the shadows from every light source was considered distracting?
If that's the case though, it's still not a good excuse at all. I generally like games being made more accessible, but I don't like it when it waters down the game for everyone else. If my guess is correct, then it should really have been an option. I was just reminded of Super Mario Sunshine letting you put on sunglasses to darken the screen after you get far enough in the game, because the sun got brighter with every Shine Sprite you collected.