This level doc goes over on how to build an Uncharted 3 mission. Uncharted sticks to more linear and scripted levels to have enough control to deliver a cinematic experience.
Uncharted does a great job of setting up pacing for the entire game and always working with the big picture in mind. In Uncharted 2 preproduction they created this excel doc going over all their levels ahead of time. In some of the missions themselves some designers would make even more detailed gameplay beats to find the intense moments for every few seconds.
Uncharted cycles through traversal, stealth, and combat areas. Some of the more complicated areas combine two or all three of these. In this flow map I go a bit more detailed on the traversal flow to help me build an elevation map [which I drew on paper which is why it's not on here, sorry]. This was helpful in Uncharted where climbing is a large part of the gameplay.
I detailed out three different combat areas and tried increasing their complexity and intensity. Uncharted uses cover based combat so every combat zone needs to design for this. The first combat zone is simplified so you can see the most rudimentary combat encounter.
I built the blockout in Maya and took screenshots to turn into top down maps for breakdowns.
An important part of Uncharted is keeping Drake in the center of action. Whenever you build a "wow" moment, have it happen right around or underneath Drake and force him to react.