Difficulty in this game was uneven. In some ways, it was the easiest Zelda game. You had Fi, which gave you lots of hand-holding. Things like dowsing, made certain sidequests easier to complete. You also had things like the treasure medal which made treasure easier to find. On the other hand, the motion controls could make certain things rather difficult and frustrating. That may be just a personal thing though. I didn't find motion controls as intuitive as some people. For example, I trouble at first figuring out just how to keep the loftwing aloft in the sky. Then there was the Levias fight. I had trouble aiming the loftwing just right.
Puzzles were mostly straightforward and easy but there were some challenging ones like the bridge puzzle.
Some things were at just the right level of difficulty for me such as the silent realms.
You also had optional things to do if you wanted more challenge like hero mode and Thunder Dragon's lightning round.
I would say overall, its more challenging than its predecessors Twilight Princess and Wind Waker but easier than the 2D games.