I haven't seen anyone mention the Sandsea concept yet, which I found amazing. The Sandsea system is possibly the most revolutionary gaming element since Portal, and I would love to see something similar (a dungeon underwater in the past yet underground in the present?) in future games.
Oh, and did anyone else notice that when present day organisms traverse into the radius of a timeshift stone, they cease to exist, yet Link and his possessions are left unfazed by the effects?
Edit: and the shield system. It's great having specialized shields which you can work to upgrade. I also love the whole shield durability system... it adds depth to the gameplay. For another thing, it was much more rewarding to receive the Hylian Shield in this game than any other, where it was basically just given to you.
I also love the shift in graphic style. I felt WM+ was a bit gimmicky at times, but I felt, overall, it was a nice addition, with a few kinks that will hopefully be worked out by the time the next game comes out. I'm still waiting for 1:1 sword and shield mechanics, with the speed and exact angle of each swing factored into in-game movement.
Guaranteed last edit: The one big problem in this game for me was stabbing. Almost every time I moved the remote in a forward thrusting motion, Link would do a vertical spin attack instead. This was very irritating when fighting all the bosses that required stabbing to defeat.