If Sony makes the PS4 backwards compatible with the PS3, then I expect the DualShock 4 will be a kissing cousin to the DualShock 3.  (Much as the DualShock 2 had only minor differences from the DualShock.)

But if the PS4 is _not_ backwards compatible with the PS1/2/3. Then there’s no reason to keep the layout which has been hanging around since the PS1. Therefore the PS4 controller can take the best attributes from all controllers.

Start with the Xbox 360 controller face layout: left analog, left D-pad, right analog, right 4 buttons. This finally makes the right analog the primary input.  Keep the select/PS/start buttons from the Six Axis along with the click feature for the analog sticks.

Steal the analog+digital shoulder buttons from the Gamecube, but move the second digital shoulder buttons underneath where your middle finger would sit to be used as triggers.  I'd suggest stealing the headset jack from the Xbox 360, but Bluetooth headsets are cooler.

Skip the motion sensor unless it’s dirt cheap. It works for the Wii because each hand is separate (so one hand can provide motion input while the other remains steady for controller input), but I’m sticking with the wing grip style which works for the majority of games.

Upgrade the rumble so the left & right motors are independent, reversible, and variable speed.  Developers will have a field day improving the "immersion".

Evolution, not revolution.