I just got around to playing this game and to be honest, I don't see why so many Zelda fans hate it. I've played almost every game in the Zelda franchise and I personally love Phantom Hourglass! The characters were fun and some of the puzzles were actually very hard. =)
It's probably my new favorite handheld title, even beating Link's Awakening!
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I think both DS Zelda games had great potential that wasn't cashed in on. I loved the touch control, I loved different ideas from each game, I loved the bite-sized dungeons, the innovations, certain pieces of music, characters like Linebeck and Byrne/Staven, and so on. I loved in particular how ST progressed the Adult Timeline Arc in a meaningful way.
That being said, they both suffered from lack of length, lack of side content and in PH's case, the Ocean King Temple's various annoyances. If they had spent 4 years making one great DS Zelda instead of two years each on two average ones, they could've had a long, lengthy Zelda that had all the best elements of those games and twice the content/interactivity. It doesn't help that at times, Phantom Hourglass feels almost like a beta for the main event that is Spirit Tracks.
tl;dr both DS Zelda games are too short and too shallow, they should've created one big awesome one, if that makes sense.