It's more environmentally friendly as less chemicals are used since less copper is etched away. It also helps prevent warping since copper distribution is more balanced across the board with copper fill (as opposed to areas with lots of copper and areas with very little). If the copper fill on top board is connected to +V or GND, it can also work for more noise immunity by working to form capacitances with the other ground and power planes.
JUst don't leave any areas of copper fill floating...make sure it's connected to a signal (preferably a low impedance one), or +V or ground.