I just finished a run of Link to the Past / Super Metroid crossover randomizer. And it's one of the best gaming experiences I've ever had. The items for both games are randomized and distributed across both games. For example, I found the first sword in Link to the Past above Samus's ship in Crateria in a secret area.
How do they deal with the linearity of Zelda games, where you NEED a certain item to succeed in a dungeon, before you can then get access to more items later? If I need the hookshot to pass the water temple, but it gives me the floating-light-boots, how am I supposed to beat the level?
You can still get the wrong items in the temple of course, it just means it's outside the temple. Sometimes you even have to go into a temple you can't beat, get an item from a chest, which allows you to get the required item outside, which then finally allows you to beat it.