Pretty much the only company that has put the d-pad above the analog stick in the last ten years is Sony.
granted, it is a move accessory, but even sony can learn.
and just about analog comfort, I think the big problem with the dual shock is the short stub handles. Make them longer and I'd be better.
For the PSP 1000-3000, problem was that it was directly under the d-pad; I understand that things under the case prevent it from having a better design, but if the nub was slightly more offset to the right it would have been a lot more comfortable.
For the PSP go, just move the analog nub higher up. Other things to be done, like not having it be a rough dotted convex piece of hard plastic with a very small range of movement, but positionally it would be fine. The old leaked pictured seemed to have the right idea.