I will say that there's no reason the L button couldn't have become a shield block for PH.
But the stylus really eliminated all the Z-targeting nonsense and still allowed for the epic big boss monsters of the 3D generation of Zelda games. I haven't started ST to see if it made any improvements. I can't see how controlling Link is difficult with this thing, and you're given total control of the boomerang, bomb destinations, etc. And drawing on the map is excellent.
But yeah, a D-pad option would be nice for those who wished for it. It's not like you're using that hand in the game now, if I recall correctly.
I wish the new Pokemon allowed for stylus movement of that kind, although it switched the whole menu over to total stylus, so I guess it's be one or the other. I also like being able to drag and drop my units in Fire Emblem and Advance Wars rather than click-clicking each step (Final Fantasy Tactics Advance 2 could've done the same, but instead made you have to tap the stylus twice for each tile movement, which is dumb as hell).