I personally loved Phantom Hourglass. It was my very first zelda title ever, and it turned me into a fan. The boss battles were revolutionary(Crayk, anyone?) and The ocean was smaller than windwakers, making it a blast. The story was also simple, and so was the music and islands.
I liked PH way better than ST. I hate using the damn train to travel through the overworld, I feel so restricted. In PH you can sail anywhere and the element of exploration is there. In ST you can still find hidden train stations but it just doesnt feel the same. The next portable zelda for the 3ds needs to drop this formula and go back to the original 2d format so you can just explore the overworld like in the original and LTP.
I actually preferred the inverse. I much preferred Spirit Tracks over Phantom Hourglass just because of the central dungeon. The central dungeon in ST was wayyyyyyyy better then the central dungeon in PH