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If there was an overworld map like FFXI/many other FFs (3d version of the classic 2d maps) that could be a neat "2.0" flying feature, but the zones are not designed for inside zone flying so I think it would just mess things up. For a 2.0 overworld map say you could land in special areas like Aetherytes, large enough Hamlets, and perhaps new areas of the lower realm that SE deems.
Lore reason will probably be about the same lines of "magic" *waves hands* lol.
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there was a liveletter a while back at one of the fan fests that specifically stated that there would be no flying in the current zones that starting in 3.0 there would be the new zone you could use the new flying mounts in and would not be useable in the zones from 2.0 to 30.0
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Not 100% on this, but heard that FC Airships would be able to fly in the 2.0 zones?