You must notice, that at least when you look at the Dual Shock 3, your arms would seem to settle to a more 90 degrees angle when you hold it, which is pretty much the natural position when you rest your arms in your lap. Also your wrists need not be angled, and then your thumbs indeed fall naturally on the analog sticks.
Were the analog sticks positioned on the DS upper, in place of the cross controller, then the "fins" would also need to be angled more inwards, as in the xbox360 controller, making the general outline of the controlle more "square" than the "wider at the bottom" as it is. But at the same time it would put your wrists in an angle.
In your pic Powderkeg, you don't seem to be holding the controller as you would when you are playing, somehow it looks like you've just put the controller in your hand so that the analog falls under your thumb in that position, instead of putting your hand on the controller. You seem to be holding it too much from the edge, shouldn't it be held more "firmly"?
In DS2 the analog sticks might not be in such an ideal position, but already there, the current position is anyway more natural than if they were upper (at least to my hands).
The shape and the angle of the "fins" do indeed make a big difference as to whare your fingers position themselves when you hold the controller. Even small alterations in the angles and contours would make a big difference in ergonomics. Therefore a controller should not be critisized or praised too much if one has not actually held and played with said controller.