First the button changes. The most noticeable relocation include the (+) and (-) buttons and the (1) and (2) buttons. The Numeric buttons are no longer centered on the controller, they are now set askew. While this appears to be purely a design change, the feel of going between the two buttons does seem slightly better when using the controller in the vertical style. As for when you turn the controller on its side, the feel becomes slightly more akin to the button layout of a SNES controller and seems to fit the ergonomics of the thumb a bit more as the buttons line up with your thumb tip's natural arc of movement.
While that change feels minor, the migration of the (+) and (-) buttons make a lot of sense. Instead of being positioned between the number buttons and the D-pad, they flank the D-pad. This makes those buttons imminently more accessible to your thumb while you are on the D-pad. When using the controller horizontally though, the buttons don't seem to be in any better of a location than they are on the standard Wii-mote since they are just as awkwardly placed. At least this way, they are close to your left-hand-thumb instead of equally out of the way of both hands in the middle of the controller.
The last button change is the Home. While this normally sits between the (+) and (-) buttons, PDP has moved it to the top of the controller, opposite the power button. Quite frankly, there doesn't really seem to be much difference as far as ease of use is concerned, and it seems like one of the main reasons PDP wanted to move these buttons out of the way was to make room for the apparently bigger speaker.
Now, while the button layout is important for a new controller, that isn't the AFTERGLOW's big feature. That is, of course, the lighting effects it can pull off. The version of the AW.1 for the Wii we got in is studded with six blue LED's and through the clear plastic case, you can see the blue circuit board to match the lights. These lights can be set to either Off, On or Acceleration. The first two modes are self explanatory, while the third changes the lights based on the controller's movements and speed.