If you are fed up with all mods/game versions using different Scenario folder, and you want to keep all of your scenarios in one place, you can do it by following these easy steps:

1. Move all of your scenarios from all Scenario folders to the main Scenario folder (C:\Program Files (x86)\Microsoft Games\Age of Empires II\Scenario)

2. Delete all of your Scenario folders (instead of the main one)

3. Run cmd.exe and use this command to create link from your mods to the main Scenario folder:
Code:
mklink /J "Source folder" "Target folder"

Here are some examples:

WololoKingdoms:

mklink /J "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Voobly Mods\AOC\Data Mods\WololoKingdoms\Scenario" "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Scenario"

WololoKingdoms DE:

mklink /J "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Voobly Mods\AOC\Data Mods\WololoKingdoms DE\Scenario" "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Scenario"

Forgotten Empires 3.3:

mklink /J "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Voobly Mods\AOC\Data Mods\Forgotten Empires 3.3\Scenario" "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Scenario"

Forgotten Empires (age2_x2.exe version):

mklink /J "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Games\Forgotten Empires\Scenario" "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Scenario"

AoC HD:

mklink /J "C:\Program Files (x86)\Steam\steamapps\common\Age2HD\resources\_common\scenario" "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Scenario"

Realms:

mklink /J "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Voobly Mods\AOC\Data Mods\Realms\Scenario" "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Scenario"

Portuguese Civ Mod III:

mklink /J "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Voobly Mods\AOC\Data Mods\Portuguese Civ Mod III\Scenario" "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Scenario"

Albanian Civ Mod:

mklink /J "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Voobly Mods\AOC\Data Mods\Albanian Civ Mod\Scenario" "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Scenario"

Age of Eagles:

mklink /J "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Voobly Mods\AOC\Data Mods\Age of Eagles\Scenario" "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Scenario"

Definitive Edition:

mklink /J "C:\Program Files (x86)\Steam\steamapps\common\AoE2DE\resources\_common\scenario" "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Scenario"

v1.6 Game Data:

mklink /J "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Voobly Mods\AOC\Data Mods\v1.6 Game Data\Scenario" "C:\Program Files (x86)\Microsoft Games\Age of Empires II\Scenario"

You can also use mklink /D instead of mklink /J, it will have the same effect.

Warning! If you update a mod through Voobly, your scenarios will be be deleted, so always keep a backup, or rename the Scenario folder before updating!