A rear touch-pad, a la vita, with some reform to the shape to allow this.
Improved vibration technologies.
Concave analog sticks
Concave triggers
LCDs on the button faces to allow for context sensitivity?
Longer battery life / wireless charging
Change of default color. We had grey in the 90s, and black in the 00s. Whites and chromes are the new flavour of the month.

Making it ergonomic would be a start.

 It's current design was meant for 2D style games (DPAD in natural/primary position still)

 It's time to update the controller, as we are now playing 3D games.

 The left analog stick is used more now then the DPAD, so makes more sense to move the left analog to the natural thumb position. Look at the 360 controller for great ergonomics. Theres a reason it won mulitple awards for comfort and ergonomics.

 The problem is PS gamers don't want improvements/changes, as they are use to what we currently have.

 Hell I was the same at first.

 The DS needs a few ergonomic improvements

1) Move left analog stick to the top

2) Make the shape of the controller fit your hand when you grab it (see 360 pad).

So pretty much same layout/shape as 360 pad BUT make 2 sizes.

One for small hands and one for big.

Sony need to remember - The controller should adapt to the hand NOT The hand needs to adapt to the controller.

Oh and get rid of those nasty L2/R2 triggers. Either replace them with 360 style triggers or go back to the normal DS2 L2/R2 buttons.

I believe they'll make it similar to the Wii U controller. You can't release a controller like that separately if you want it to be supported and we all know Sony and MS are going to have their versions of the Wii U controller eventually if not at first.

Don't change it. The dualshock is the perfect design. If they change L2/R2 again, I wouldn't mind but keep everything else the same.

I would keep the basics the same. I'll just repeat what some other users have already said. Make the analog sticks more durable. The Dual Shock is better, but I had to replace a couple Six-Axis controllers after playing Resistance way too much back in the day. I would also work on the triggers. They're workable, but awkward at times. As other have said, I would just make them more concave.

Overall though, I like the PS3 controller, so they don't need to change much.

Then it wouldn't exactly be a DualShock, would it? :P

I want it to stay the same it's my favorite controller out of all game generations. I just love the way it feels in my hands.

i would like it to be the same as then DS3. its perfect the way it is tbh.
The only difference for me i think would be good is if they build a mic into it so it also works as a headset like the Vita.

If it ain't broke don't fix it. DS3 is perfect.

Evolution, not revolution. That's all.