More Taxi System oddness
In Dragonblight, to get to Warsong Hold in Borean Tundra it tells you to fly to Dalaran, take the portal to Orgrimmar, then take the Zeppelin to Warsong Hold. It did this right up to the border with Borean Tundra!
We use an average wait and flight time for zeppelins and boat so the taxi system probably calculated it to be faster than using the flight master and it is likely true even if its only by a few seconds.
Do you mind taking a screenshot of the map route and post it, I don't have the right character to test for that.
Another issue is that when I'm in Stormwind and want to go to Outland, it suggests I fly to the Blasted Lands instead of just take the portal in the Mage Tower. There is no way that flying there can be faster.