What they COULD do, and I don't normally like to use the ideas from other MMO's because I'd like SE to do their own thing, BUT -

Guild Wars 2 is going to have a Fast Travel system as well, which is actually free to do. However, they're going to give incentive to players to run there because you get some sort of bonus for exploring and walking/running to where you want to go (Not sure of the bonuses yet). Now, I'm sure you have to have been there first, but it gives people the choice, as well as the incentive to do some adventuring.

While I hope FFXIV stops using the Anima system, IF they keep it I'd like to see some incentive given to adventurers to travel there instead of teleport.