I like the idea that hidden skills could make enemies more difficult if learned. I don't really think of how Zelda enemies worked harmoniously to provide difficulty but I think it's true! It made the classic 2D games more difficult and promoted more reflexive gameplay that was enjoyable.
I think one feature that recent 3D Zelda games lack (haven't played Skyward Sword or Majora) are traps and deterrents in dungeons. A Link to the Past had a variety of these in the game including plenty of spikes blocks, holes in floor that even send you a floor down to impede progress, blocks that shoot fireballs, a trail of fireball, invincible jnyxes that steal tiny amount of your magic and health, and moving floors.
And if you think about, dungeons are suppose to have traps and deterrents! The only dungeon that seemed to have plenty of traps and deterrents in 3D Zelda was the Shadow/Sheikah temple in Ocarina of Time (haven't played MM or SS). 3D Zelda games seem to replace traps and deterrents with puzzles instead. However I think a good balance between traps, deterrents, and puzzles would make 3D Zelda dungeons more challenging and new!
Edit: Sorry for not formatting my wall of text earlier!
