The problem is you can't run with the DPad. You have to hold a button down to imitate it. So even with the 3DS analog stick, it'd still have the same problem.

That single handily broke the game for me. It doesn't feel good to use the touchscreen as an analog stick.

It doesn't work like an analog stick, though, it works like a d-pad. It just maps to up, up-left, left, down-left, etc of the d-pad, like in any other DS game played on the 3DS.