Is there any chance you could add the ability for server OPs via commands to give scrolls NBT data (like teleport coords) so that a particular scroll can only be used to take you to one predetermined location. Not the last waystone activated but as an item to teleport you to the next objective that you have not been to before. It would be nice if you could also automate creation of these scrolls using command blocks instead of a player (OP) having to create it manually.

The latest 1.12 version can do this now. Example:
/give @p minecraft:warp_scroll 1 0 {WarpScrollTarget:[-5,64,5,0]}
would give a warp scroll that teleports the player to x:-5, y:64, z:5 in the overworld (dimension id 0).