One of the trickier things is having the rewards being still worth the trouble of solving the puzzles. Generic upgrades aren't as compelling when you have to go through a brain teaser to get to. As a result, I feel the first dungeon has the most items in it, the second has a couple that open up the rest of the game, and the final dungeon is sort of the big puzzles left in the main dungeon and a final Mini Dungeon which, while it doesn't have as much, does have a few challenging things.
Since this game lacks a "Boss" battle, I think the final dungeon's riddles will be more like a "Boss"