I think they should keep anima when other travel means are released, but do something a little different with it.

Maybe they could limit it to teleporting to capital cities and aetherial gates (not aethyrite crystals), making its function similar to what it is now, but placing more emphasis on using anima to ease population overflow from popular behest camps. Or they could place a cooldown on how often you can use anima when porting to certain places.