This addon missing the Mistfall Village flight path is a Blizzard issue. The author makes use of the tiny flight master icons on the normal map to place a clickable flight path icon. Unfortunately, while the taxi node does exist, the little yellow "neutral" icon does not, along with the taxi node not appearing in the map provider data. Blizzard forgot to fully mark this new flight path, even though it's on the default flight path window.

I was able to locate the node data on wow.tools and fashioned some code to force it onto the Vale of Eternal Blossoms and Pandaria maps. Given the size and position of zone maps, this new node will also appear on your Dread Wastes and Valley of the Four Winds maps.

Go to your WoW install folder and open the file _retail_\Interface\AddOns\WorldFlightMap\WorldFlightMap.lua in any text editor. There are three pieces of code to place in three different spots:

Find this first set of lines:

end

function WorldFlightMapProvider:OnEvent(event, ...)

Place this block of code BETWEEN THE LINES as shown:

end

local MVantiloop={}
local MVposition={
    [376]=CreateVector2D(0.3020,0.1563), -- Valley of Four Winds
    [422]=CreateVector2D(0.8680,0.2045), -- Dread Wastes
    [424]=CreateVector2D(0.4679,0.5793), -- Pandaria
    [1530]=CreateVector2D(0.3891,0.7278), -- Vale of Eternal Blossoms (8.3 version)
} -- 8.3 fix

function WorldFlightMapProvider:OnEvent(event, ...)

Find this second set of lines:

        self:RemoveAllData()
    end
end

Pay attention to how many ends there are.
Place this new line DIRECTLY BEFORE THE FIRST END as shown:

        self:RemoveAllData()

        for k,v in next,MVantiloop do MVantiloop[k]=nil end -- 8.3 fix

    end
end

Find this third set of lines:

                pin:SetShown(taxiNodeData.state ~= Enum.FlightPathState.Unreachable); -- Only show if part of a route, handled in the route building functions
            end
        end
    end
end

Once again, pay attention to how many ends there are.
Place this block of code BETWEEN THE FIRST AND SECOND END as shown:

                 pin:SetShown(taxiNodeData.state ~= Enum.FlightPathState.Unreachable); -- Only show if part of a route, handled in the route building functions
            end

            if MVposition[self.worldMap.mapID] and not MVantiloop[self.worldMap.mapID] then
                for k,v in next,MVantiloop do MVantiloop[k]=nil end
                MVantiloop[self.worldMap.mapID]=true
                WorldFlightMapProvider:AddFlightNode({
                    state=1,
                    name="Mistfall Village, Vale of Eternal Blossoms",
                    position=MVposition[self.worldMap.mapID],
                    nodeID=2544,
                    slotIndex=42,
                })
            end -- 8.3 fix

        end
    end
end

Save the file then reload the game if it was running and voilà! A new flight path! It won't immediately show when the map opens, but clicking to another zone or to the continent will make it appear. I wasn't able to figure out why.

(god, curse comment formatting sucks)

In reply to Istumi:

 That was my worry when I was looking into the flight data. The state (it's 0, 1, or 2 depending on nearby flight paths) and slotIndex parts may be dynamic. When I learned that new flight path, I had already learned every other flight path on Pandaria. I don't know if the slotIndex is supposed to be 42 for everyone or 42 as in the 42nd flight path when the data is enumerated. If you don't have all flight paths learned, slotIndex may not be 42 for you.

In reply to BujuArena:

 This is a bandaid fix until Blizzard decides to fix it. As Istumi demonstrated, it won't work for everyone. I'm also not in the business of forking someone else's code and then hosting it, I don't care what license it has. If you are unable to make the simple copy/paste changes above, I don't know what to tell you.

In reply to BujuArena:

 I wasn't offended, and I didn't mean for my comment to come off the way it did. I know how GitHub works, but I took your suggestion as hosting a fan update, which I'm not a fan of doing. I feel sharing details on how to edit the code that someone has in their possession is a much simpler method of offering temporary fixes than directing someone to my GitHub.

Quote from Fiercepook >>

Confirming that the new Mistfall flight path is still not showing in WFM, but does show if you disable the addon.

 

This was the only flight path added in the new zone overlays of Uldum and Vale of Eternal Blossoms. I imagine that it being missing has something to do with that, possibly because the addon isn't recognizing the "new" Vale map. Normally it's not an issue because the flight paths and maps are all laid out exactly the same regardless of the version of the zone that you're in, but the "Visions of N'zoth" version of the Vale has this one difference, the extra flight path point in Mistfall. 

 

Unfortunately I don't know enough about addon coding to say what can be done to make the addon recognize the "updated" Vale map.

Confirmed. Any would-be helpers out there willing to tell us how to manually add the FP?