When I first played Phantom Hourglass, I felt a lot like I did when I first played Metroid Prime 3 - I felt like the controls did not work, and that Nintendo had made a big mistake. But like MP3, I gave PH a little more time, and now everything feels second nature.
I just beat the 2nd dungeon and I think it was better than the first. There are definitely some puzzles you have to think more about, mainly because Link is able to do much more than in past games.