Here's a thought.
We already have set waypoints in wilderness areas, which we log as we travel through them. Explorer points.
Why not allow the Teleport spell to take us to those? We can select the area, then select an explorer we've already gotten within that area.
It covers the "Only teleport to places you've been" idea, yet doesn't break it by allowing much exploiting. It doesn't require the devs to code waypoints into the areas, or ways to set your own waypoints, since the waypoints are already added to the areas. It's just a matter of adding them to the teleport target list.
Of course, I'd settle for adding more areas to teleport(Korthos, The Twelve, the entire list of Greater Teleport locations, the Red Fens, Lordsmarch Plaza...), but if we're already adding new locations it would be nice to give the explorers a use.