The main flaw is having aetherytes in open areas, rather than walled off with a gate.. it is essentially an international port. Ul'dah's main aetheryte has been handled the best in this case. To be really secure, you'd also do the same with Aethernet shards, or don't connect the shards with the main aetheryte (if that's even possible). It is possible to travel unattuned to an aetheryte, although not many people can do so and live (the WoL has done this).

That said, given that it's possible to destroy an aetheryte mid-teleport, it's evidence that teleportation is not instant, and that there is some way to tell if people are coming.