I want Zelda to Emulate the Resident Evil Series in a few ways actually. Not with zombies and stuff (although that would make for a sweet minigame), but rather with limited ammo. With the Resident Evil series (especially before RE4), you had to be very careful with your ammo and supplies as there was a very very limited amount. While I realize that since Link has a sword, the use of ammo such as bombs and arrows isn't exactly needed nearly as much. But I want this to change.
I want to actually have to feel the need to stock up on supplies from the Zelda GoodStore, before I venture off onto any quest. The only Zelda game I ever really felt I had to buy stuff was Majora's Mask and that was probably because each time you went back in time, you had to grab supplies. Granted you could still just go through the overworld and dungeons and start killing things for supplies. Supplies are too abundant in grass and areas.
Often times if there is a puzzle in a Zelda room, the required supplies will be there as well. Now I know this helps to serve as a hint and to make sure you don't have to backtrack to get supplies, but I feel it makes the games too easy. By having to stock up on everything beforehand, you will have to think really hard before just shooting an arrow at something and hoping it works.
This could also open up some really interesting stealth sections. Say you were out of bombs and there was an enemy that could only be killed with bombs in front of you, well maybe you could try sneaking past it like in The Wind Waker in order to avoid taking damage. Sure you could probably just run past it and only take a few hearts worth of damage, but that is also my second point.
Like Resident Evil, I want the damage multipliers to increase. If you get hit by an enemy in most modern Zelda games, there's not really any penalty. However in Resident Evil, if you get attacked by two enemies, your health is most likely going to be red and you'll have to use some sort of herb or first aid spray which are also scarce. Zelda enemies usually don't do enough damage for me to ever really bother with blocking, especially with Skyward Sword. Since the enemies never really attacked in that game, I found it better just to attack as that was a much better defense then bothering to use my shield.
Overall, there is a lot that Zelda could learn from the Survival Horror genre. The games could have some scarier Dungeons and areas (not all just some), they could have enemies that cause meaningful damage, and they could reduce the amount of supplies that enemies and grass drop. I'm a huge fan of Resident Evil and I would love to see some of these elements implemented in Zelda WiiU and Zelda 3DS.