While it's easy to view Phantom Hourglass as the successor to The Wind Waker, in reality, it's just as much a direct descendant of A Link to the Past, due almost solely to perspective.
Over the years, I've played a number of games where the control schemes were complicated enough that if I set the game down for a week and came back, there was an irritating period of readjustment. At the same time, in those cases, it was generally the case that I set the game down because I simply didn't have time to play it for a while. The strange paradox of The Legend of Zelda: Phantom Hourglass is that the control scheme is so refreshing and intuitive, I imagine I could have spent months away from it and picked up where I left off, yet I found myself taking long breaks from it because I felt as though I needed to.
As has been discussed elsewhere, probably the greatest flaw with Phantom Hourglass has to do with a single temple that must be revisited at several points in the story, as one gets further into it each time. This wouldn't be so bad except for the fact that previously conquered levels must be replayed to get to the new content. This, coupled with a time limit, really limits the way in which these portions feel like legitimate parts of a Zelda game, and Phantom Hourglass suffers for it. Whenever I realized I had to go back to that main temple, I generally sighed, closed my DS, and took time out to play something decidedly more fun.
Fortunately, this isn't any sort of deal breaker, as the rest of the game is crafted remarkably well. I remain a huge fan of The Wind Waker, and find the art style as charming here as it was there (though for the first time ever, I found myself wishing the DS had a touch more horsepower when the camera perspective was close up). I enjoyed sailing the seas in The Wind Waker, and those sections have only been improved here. The boss battles are fairly inventive, and the dungeons are well-designed, if a little on the easy side.
But the star here is clearly the control. Not only is controlling Link with the stylus effortless, but it makes low-level combat both straightforward and fun. The ability to draw the path of items like the boomerang and grappling hook makes their use much more precise. Further, there are items, like the walking bombs (Bombachu), that seem to require the stylus as an input mechanism to be at all realizable. Finally, I cannot overstate how helpful it is to be able to take notes and mark maps at any time in the game, particularly as someone who is compulsive enough to keep notes on more complicated backtracking games as I play.
...and you thought the boomerang was useful before...
It seems appropriate to view the histories of Zelda, Mario, and Metroid as having two distinct paths. In the case of Zelda, until its debut on the Nintendo 64, the franchise was largely represented from a top-down perspective. Similarly, Mario and Metroid were side-perspective games until their Nintendo 64 and GameCube outings respectively. Those leaps to the 3rd dimension were deservedly lauded for not sacrificing the fundamental feel of their two dimensional forebears. But games like New Super Mario Brothers, Metroid Fusion and now The Phantom Hourglass demonstrate that the two dimensional presentation of the older games has yet to be forgotten.
So while it's easy to view Phantom Hourglass as the successor to The Wind Waker, in reality, it's just as much a direct descendant of A Link to the Past, due almost solely to perspective. Viewed from that lens, the changes to the control scheme are largely what prevent the game from being as much as a rehash as it could be argued most Zelda games are. Like the Wii-specific controls for Twilight Princess, it is the controls of Phantom Hourglass that set it apart from its predecessors in ways that inevitable graphical upgrades never could.