In the mission editor on the flight properties dialog, have a combobox that lists existing uploaded skins for the selected plane type, or the selection "Default".
If a skin is chosen, when the mission is run, if the player has that skin downloaded, it uses it for that flight. Else it injects a text message that "Skin xxx needs to be downloaded" and then simply uses the normal default.
Alternatively, when the mission is started if could check the mission def against local skins and ask if the player wants to wait while the skins are downloaded.
