I think a FATE rework is the solution here. Making it difficult to travel won't go over well with a lot of players, especially with stuff like taking away flying.
Make FATEs more difficult and more interesting instead so that there is some kind of interesting open world content. Players that don't want to deal with them can go around while those interested in participating can join. These FATEs might also have some relevance to the map like influencing the appearance of special vendors or locations.
This could be further expanded with optional open world areas that are meant to be dangerous. Places where the MSQ doesn't necessarily go but has some value for players, like dangerous enemies with better drop rates for useful material. I'd rather have this over the shared FATE system and gems that has you grind mindless FATEs for what feels like an eternity.
