I'll have a look when I jump on later. I'm happy for the direct option with a universal return rail but that would need a fair amount of planning and infrastructure, although time is plentiful at the moment lol! I'd be correct in saying you're suggesting a tunnel with two rails - one to and one back from the destination? My only real concern with this system is if a player wants to get to a farm/location that's on their "half" of the nether (you to the guardian farm for example) you'd have to travel to the Nether Hub before travelling back to the farm. We'd certainly need to do a fair amount of clearing out at the Nether Spawn area, although be careful, I'm fairly sure it's close to the top of the Nether caves!
What could be fun is having different tunnel designs depending on destination. Let me get my Voxel Map up and show the potential destinations etc and we'll take it from there.
Planning and putting the infrastructure in place will be hilariously difficult, but that's where the fun is, I can see it being somewhat rough and ready and refine as we go. For midway branches like myself to the guardian farm, I'd probably just create a separate single branch line outside the main network. Different tunnel designs per route would be a great idea, make routes instantly recognisable.
After looking at your map waypoints i think a hybrid design of both our ideas might be preferable, we could still have the central station with multiple branches but on some routes have your way-station design where it makes logical sense and is limited in no. per branch. That will simplify the design but not making journeys too onerous. Let me know what you think.