PH's problems weren't their controls, not at all. Hataz gon' hate here, but the controls worked exceptionally well. I wouldn't say they were better, but a fully functional Zelda title with purely touch controls is pretty impressive.
No, it's problems were it's horrible dungeon design, lack of effort in the sound department, and it's buttfuckingly horrible repetition of design ideas. Touch screen controls are fine, but a continual repetition of "hey, you can use your stylus to solve this puzzle that you've already solved thirty times before!" is just lazy, lazy development.
I've been of the opinion that PH was very much a proof of concept. It's was fairly successful but lacked most of the charm and strengths of a true Zelda title. I'm hopeful that ST takes things much further, but I won't be betting on it.