Some IGN interview with the hardware designer said that the original will most likely be the final. I'll go hunt it down now, but I'm hoping its true, I doubt I'll use the D-Pad much anyways.

Found it, here ya go.
"IGN: Knowing what happened with the DS, when they first showed the DS back at E3 2004 -- it changed. When it came out there were a number of differences in the form factor, and some other more subtle changes. Are we going to see this exact 3DS system at its launch, or will there be subtle differences?

Konno: I think you should be looking forward to this one right here."

http://ds.ign.com/articles/109/1099199p1.html (on page 2)

Yea bell i actually remember reading that, it will be interesting to see how it finally launches, whether they keep this design or not

That's a big problem with DSi, I've done that so many times!

They should do this: keep the design how it is now, except move the A/B/X/Y buttons down and put a slide pad where they used to be. That way, there would be two slide pads, they would be parallel, and the d-pad and face buttons would be parallel, making playing DS games more comfortable/natural.

they should get a second slide pad in there and make the bottom screen bigger

Going off what NotEnoughGolds said, perhaps it would be best if there was one side with a D-Pad and slide pad and the other side having the abxy buttons and another slide pad, with both sides being rotateable and flippable (abxy on left, etc.). I think that could work well, though Nintendo'd probably have to sell replacement pads then.

ok 1st of all DS games use... the touch screes for camera movement in FPS games. & i dont see that changing on 3DS. what i do see is slide pad for movement, touch screen still being used to move camera in FPS games, R & L button to shoot, D PAD,to change weapons. ya know that whole thing, the A, B, X, Y buttons also, & options to move around with slide pad or D PAD in games. also the accelerometer & gyro sensor can be used to move camera.

I prefer the one with the analog stick on the left. I think that would pan out better for the controls. I also think that we should have eight buttons instead of just six to allow more core games.

I think making it so the stylus slot was on the side of the 3DS system would be technologically fils-able.

Raise the d-pad by a teeny weeny smidge, and place the headphones input on the far bottom right side instead of the middle