I think it's fine the way it is actually. Maybe add a touchpad on the back.

Actually make a good controller? I detest their controller. Every time I buy a Sony console I have to buy a 3rd party controller. Seriously it's 2012 and the PS3 STILL has a d-pad as it's primary input.

Think about that for a second. The PS3 has a d-pad as the primary input over an analog stick. Before anyone tries to debate this and say how it's opinion which is the main input. Keep in mind that the controller is basically identical to the PS1 controller. A controller that only had analog sticks added after being designed. The entire controller form factor was built around the d-pad. The controller exists in a form without the analog sticks at all.

Make analog the main input, put some better analog sticks on there, turn the triggers into proper triggers and for goodness sake redesign the hand grip bits. The hand grips have always felt like less part of the controller and more like the type of clip on things you get for the PSP etc. Then when they have a good controller they can worry about adding touch panels etc.

The DS was quite good for the PS1 generation, awful for the PS2 generation but for the PS3 generation? It's just an embarrassment. The only reason it's kept is because people are used to it. People were used to the SNES controller too, but the times they are a-changin'.

If it stays similar to the current design they need to have two controllers , one the same size as now and a larger version ,then they can continue to box the original and sell the larger one separate, as to its features/design a lot of that will depend on what they see as the future direction for game interfaces and its incorporation, either into the present design or a complete redesign, in that regard they most certainly will be watching the WiiU and getting feedback on the use of the vita as a de-facto controller plus what ever else might be on the horizon.

Make it shaped like a boomerang.

Really they should use the psv, with hand grips and add triggers. PS4 and a vita in every box. Maybe the hand grips can house the buttons and break off the vita so they can keep up with the motion gaming trend. They could sell the grips in different styles and sizes so they can please every one (well most of everyone).

new shape, size is about the same as x-box's it just the depth

if i were sony id add another face button, for example in uncharted cover and roll are the same button if there were an extra face button you wouldnt have the issues of going into cover when you really wanted to roll, and i feel lot of other games seem to be maxed out with the current 8 button scheme

more durable current ps3 controller at least for me has a lot of flex, the internal for the sticks have issues there not smooth theres like clicking noise when going back and forth at certain degrees

i have no issues with the stick position not being concaved, and the triggers i guess im just used to it

I would like it if you could split and re-combine the controller whenever you feel like it. It would make it easier to use for motion controlled segments in games. And sometimes it's more comfortable not to have to hold your hands together all the time. Wii mote and nun chuck is a pretty comfortable setup, just why didn't Nintendo include a 2nd analog stick doh! 2 nun chucks that can be combined would be nice.

Maybe slightly extended the dual shock so there can be buttons under your middle and ring finger on the bottom of the controller. RPGs can use some more configurable hot keys.

I would be happy already if the improve the triggers L2/R2 and provide better grip on the analog sticks. Do not swap the left analog stick with the d-pad. Last time I checked my hands are symmetrical. I like it the way it is.

Make bigger triggers and don't touch anything else.

okay nothing is really wrong with it now, but if i were to change anything it would be...
make it a similar shape to the xbox controller (without the battery pack)
make L2 and R2 triggers (still keep the option to have R1 be shoot)

leave the D-pad alone
leave joysticks alone (i dont really mind concave, but i prefer convex)
DO NOT, i repeat DO NOT change the placement of the joysticks and d-pad. it makes no sense to have one joystick up and one down, its weird and awkward.
i will be forced to buy a normal controller from a 3rd party if this happens

Sounds like you're ruff on your controllers. You might have a busted one if you have a clicking sounds coming from your sticks.