Just beat the game...
Phantom Hourglass NEEDED to have touchscreen controls. There, I said it. Despite the 3D engine, PH is essentially a 2D Zelda game and as such, needed to be something different from A Link to the Past. For me, LttP was the ultimate 2D Zelda, the epitome of its design. Every 2D Zelda post-LttP failed to capture the same feeling. That said, I appreciate and applaud the decision for touchscreen controls though the mapping items to the shoulder buttons was an welcome option.
Still, the new control method does not itself make the game original. Over half the game is typical Zelda fare. Same items, same puzzles, same structure (go to dungeon-->find weapon+keys-->beat boss-->get shiny thing-->repeat until final boss) and so on. The controls are also not perfect. Close, but still not perfect. There are times when the game doesn't register input. Not enough to ruin the experience, but it's still a minor nuisance.
The story was weak, but no surprises there (Zelda with a weak plot... you don't say?). It was kind of like the plots of Wind Waker and Link's Awakening arguably the 2 strongest Zelda plots combined into one much lamer storyline. Ocean King's true form = Fake Wind Fish.
In conclusion: Good game, weak story... most original Zelda in a while though not by much. Touchscreen controls are nice, but they don't change the series which is still too attached to its same old design and structure.