That's the worst part about A Realm Reborn...mandatory teleporting!
In all honesty, I think the teleport system we had in 1.0 was perfect, aside from not actually having to run to the Aetheryte/Gate for the first time. Lower the amount of anima given out during Hamlet and it'll make teleporting feel limited again. I never understood why having the option to move around quickly is such a bad thing. If you don't want to use it, don't use it. I chocobo everywhere unless I have to be somewhere quickly. Not a single part of my game was affected by someone using their anima to teleport themselves around.