I'm a bit torn. I liked the Hidden Skills becasue they were realistic - they fit with a semi-realistic game. They're solid, physical skills that a very skilled swordsman can master, so they fit with the "grit" of TP.
Yet, I HAD SO MUCH FUN WITH THE MEDALLIONS! A Link to the Past's Medallions were awesome - calling down explosions, lightning, calling up earthquakes... they were just powerful fanf so, so much fun. I loved Bombos, best, I think. Fire! Explosions! Whee! Seeing them in 3D would be absolutely wonderful.
I think, in a future game, since they haven't been trotted out for a while, I'd like to see the magic Medallions.