Sorry, I think you asked for specifics and I gave you game philosophy.
I have not played a Zelda game in a while but these are the aspects I think were great:
the collection of unique weapons that were relevant and useful. In many games the intermediate levels are just power ups that do not seem relevant to fighting the level boss. the gradual collection of weapons I think kept the player engaged. I especially like the hook shot and of course bombs are always good. The controls were usually very simple, you did not have to learn new controls for each weapon.
It seems that you are interested in making this type game so here are some thoughts on what might make this type of game better:
Increase the NPC AI. One of the great things about the Call of Duty series is the way the NPCs have improved. Now the enemies run away, hide,return, attack and the squads seem to provide real back up Increasing the AI in a any game would be a real improvement. Storyline branching. If the character choices have an impact on the story line then it would be a much more immersive experience.