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From what you're saying mechanics need to fit to the design of the game. 3D World because it is contained and focused you just need to add the things to a small box. Zelda instead separates these small boxes in shrines and leave the main world be like a toolbox in which you can mess around with things even if it looks odd.
But also open worlds in a way have more cohesion in regards to space. You technically travel from one place to another, while linear games, jump you around from a place to another. Which may be why that despite 3D World has harder levels than Odyssey, there's less cohesion, I mean even the worlds aren't thematically tied in terms of levels. On the other hand, Odyssey gets a bit emptier as you conquest each moon.