You really can't compare Zelda to Uncharted because Zelda is a game that is designed around the game whereas Uncharted is designed around the story. Zelda continuously builds on gameplay ideas testing the players mastery of them.
The gameplay in Uncharted is repetitive because there is no progression in the gameplay ideas. In Uncharted you are introduced to an idea and repeat that idea over and over with no progression in the mechanics. You never feel threatened or challenged. You will push the same crate over and over. You will swing across huge chasms over and over. You will traverse by spamming the jump button. Everything is at a superficial level and Naughty Dog never asks you to show mastery of any of the gameplay concepts.
It's really getting down to game design and the progression of ideas. Mario is not a jumping simulator. It introduces you to an idea early in the level in a non threatening way and you have to demonstrate mastery of that idea by the end of the level. If you don't, you will die.
See basic Mario level design:
https://www.youtube.com/watch?v=ZH2wGpEZVgE
Uncharted never does that. Instead, progression is done by flipping pages through the next story element.
For example in Uncharted 4, you are introduced to the rope and will spend the entire game doing the same mechanic over and over. Sliding down a ramp and jumping across a chasm. It never progresses beyond that and you never feel threatened or challenged with the game mechanics.
Going with the Indy Jones theme, you can easily use the rope mechanic to build on gameplay ideas by designing a trap that Nathan has to get through using both the rope and the traversal mechanics. Here you can really test if the player has mastered the rope mechanics.