My own suggestion is to make fewer aetherite points, but either get rid of anima entirely, or make it regenerate much faster (right now, quests require a lot of traveling through repetitive terrain, so everyone uses anima...yet it is possible to run out VERY quickly). Teleportation, in and of itself, isn't the issue. It only severely cheapens the experience when there are way too many places you teleport to. As long as players are still required to do some traveling in order to get to their final destination, I see no problem with it.

It also might help to put in some sort of on-rails transit system that isn't instant, but is faster than chocobo and still allows the player to enjoy the environment. Flight paths, for example.

Moderation is key. It doesn't have to be all one or all the other.