I agree, the analog nub sucks. Its too small, and I hate the feel of it, like how its hard and has that gridded feel. After using it for a while, it feels like my thumb nail is about to come off. Of course, its not, but that's what it feels like. I have high expactations on the 3DS' slide pad.
I also hate trying to use the d-pad while using the analog nub. Its not much of a problem pressing down on the d-pad, but to press anything else, you have to take your thumb off the analog nub, which causes problems when im against a group of enemies or a boss. I actually think it would be a good idea to have the d-pad under the main buttons, but on the PSP it wouldn't fit unless they completely redesigned it. It would work for the 3DS just fine, but they decided to put the d-pad under the slide pad instead of the buttons, which sucks. If the d-pad was under the buttons, it would make it easier to change commands while using the analog, or change the camera while moving your character with the analog, for games that use the d-pad as the camera. It's not like you use the buttons while using the d-pad anyway, so it would make more sense to have it under them. so you can use the analog while using any of the other buttons.