In 1.0 you didn't use gil to teleport... you used Anima, which was a self-replenishing but limited resource and different aetherytes cost different amounts of Anima, essentially to gate how far and often you could teleport. The Lore resoning for the change in 2.0 is that the Aetherytes in Eorzea were damaged following the Calamity, and the City-states took on a large loan from the Syndicate which is paid as a tax for teleporting (I believe Koji Fox said to just assume there's a friendly attendant taking your money at every Aetheryte Plaza, don't think to hard on it).

In gameplay it serves as a money-sink, since there's already too many ways to get gil for nothing, and telportation, repairs and such serve to keep that gil from wrecking the economy.