For me the top two were the Arbiter's Grounds and the Sandship. They both had great designs. Although, I give a slight edge to the Arbiter's Grounds, because it had the better dungeon item (the Spinner) and boss (Stallord). The Sandship's boss, Tentalus, was a little weak, and the Bow and Arrow wasn't really used for anything special. The Spinner was a great idea, and it was put to good use in both puzzles and against Stallord; it's just a shame it wasn't put to more use outside of the dungeon.
I'll also say that the Pirate Stronghold was a cool concept, but it wasn't executed very well. The coaster was cool, but the stronghold didn't follow very well; it felt somewhat boring. It could've used some more substance; it felt like the entire time you were just taking a Timeshift ball from one place to another.