Firstly, why do we have to control Link with the stylus if there's a perfectly good D-pad on the system? Some of the touch screen uses for items were genius, but controlling Link with the D-pad would have been much better. That's not my biggest complaint with Phantom Hourglass, though, and that's not the reason it wasted its potential. After every dungeon is completed, players must return to a central dungeon called the Temple of the Ocean King. New floors then become unlocked, but to reach those new floors, players are forced to re-do ones that they've already completed, making for a highly repetitive and frustrating ordeal.
I can't really argue with any of that. I generally liked Phantom Hourglass, but the one pain point really, really freaking hurt.
Source: iNintendo