I figure the important things to do in advance are figure out basic minimum standards for subways to have to be recognized, and get a general idea of where major landmarks/cities that should be connected at some point will be.
For the guidelines, I am thinking something like a 3x3 minimum tunnel (How much room do horses need? We might need to increase that if we want people to ride down them). We would need a maximum allowable rail spacing (1 every 38 is the most efficient, but that is also a pain to count out. I think I've used 1 every 30 on some of my personal rails just to make it easier to lay, and to counteract any random lag slowdowns). With iron and gold farms, resources shouldn't be as hard to come by as they were initially.
I'm also probably going to take advantage of all of the lessons I've learned in making multiple map iterations, and make the working map I edit a 10,000 x 10,000 pixel map. My last map attempt is
here, and writing small enough to not take up too much room made it too hard to read. I will probably also keep all subway in black, skyrail in blue, and netherrail in red on the map, so they can be distinguished.
For the skyway, I think we would want to mandate something like access points every 50 blocks or so, so people just wandering around can get up to it without making dirt columns. However, I think the skyway would probably be lower priority than getting the basic subway in. Once that is done, skyways can have some real effort devoted to them, but only after we have the basic utilitarian aspects of the subway done.
For junctions: while the redlight system is neat, it takes a lot of time to setup. I think it would be better just to have something very simple at the major junctions, and once the subway is more together, add whatever random extras to the junctions.
We will also need to figure out an acceptable way for people to link their private stops into the main subway. Whatever it is, it will need to not bring the mainline to a stop, so possibly something that slows it a little, and has a button that temporarily diverts the rails (timed, so the next people don't get diverted).