I think most people would agree with me that "Clear" missions and their variations are low key annoying - mostly because there is a way better mission type - "Fetch" - that allows player to decide the level of engagement with location on their own.
Having to clear all zombies is maybe a good idea on paper, but in reality it is more bothersome rather than interesting. Most of the time they just take too long and force player to midlessly run around the location looking for the missed zeds, and sometimes (very rare though) may bug out and hide zombies somewhere and even force player to abandon the mission (happened to me once).
I think fixing that can be achieved by replacing that type of missions with new type: "Eliminate Target".
ET would work in same way as "Fetch", but the goal will be killing a specific enemy:
The target would spawn in main loot room (or random room, like supplies in "Fetch" missions) and it will essentially be a miniboss of location - either a stronger zombie than current game level (irradiated zombies, soldiers, etc.), or location specific miniboss (like Grace, for example), or a specific group of zombies in specific room.
The idea is that player wouldn't need to kill all zombies in location, but only specified target - and seeking this target out would be as easy and uncumbersome as finding supplies on "Fetch" missions.
That way players will be able to decide how much they want to complete the locations on their own, without need to spend time on finding all of the zombies.
So on later tiers of missions these types could be easily combined into "Fetch/Eliminate Target" to replace "Fetch/Clear" missions - locations would simply have two separate goals.
I believe that small change will drastically increase enjoyment of mission grinding process.