Instead of requiring to activate/enable waypoints it better to set a character requirement to them(level 20 can use Waypoint 14 and below.).
Alternative would be allowing free waypoint travel realm-wide: making movement and exploration much easier. More waypoints in a single area could enable quick travel to/from remote destinations and quest areas.

Waypoint Skill: An utility skill that allow you to move to any waypoint in the system, as if a portal to that waypoint was used. Replaces "Town Portal"/"Return to Nearest Town" abilities.
Custom Waypoint:an ability to set an area as player-designated waypoint, which can be added to waypoint list at "Custom Waypoints". Amount of Custom Waypoints would be proportional to Waypoint skill level.

Mobile/Personal Waypoints: Game could include Waypoints on ships, flying islands, transports or bound to specific player designated as leader(of clan/party) as custom waypoint(using it a clan can gather to exact location very quick).
Waypoint as Teleport: Removing most restriction on custom waypoints, it can serve as Realm-Wide teleport:
1.Assigning waypoint to raw locations (e.g. 100045,139123,24) from UI elements like monster spawning area and teleporting to it using the new custom waypoint.
2.Simply using waypoint system with commands.
/teleport_to x,y,z (create a Last_Recent_Waypoint and teleport there)
/waypoint_add x,y,z name_of_waypoint
/waypoint_remove name_of_waypoint
/waypoint_to name_of_waypoint (teleport to there)
Waypoint Restrictions: To mitigate any abuse a character could be restricted to N waypoint uses per hour.