I'm for the subway, both for function and aesthetics. And lemme preface all of this by saying I'm somebody with extensive experience both digging out long tunnels and building long aerial structures.
Digging out a subway generates cheap resources (cobble, iron, coal, etc.) whereas building a skyrail just consumes resources. A subway is also more secure and safe for travelers, since if mobs spawn due to torches being stolen or wander in from connected dark areas, they can be more easily dealt with in an enclosed tunnel than on top of a high open structure where creeper explosions or skeleton arrows may (depending on the skyrail's specific design) have a high risk of knocking players off. Also, since the extensive subway infrastructure in private realms will be preserved, it'll be much quicker and easier to rebuild the missing sections and expand further.
Aesthetically, a subway is much less obtrusive and simple to build and connect, whereas a skyrail requires unobstructed airspace, and for all players contributing to it to be able to memorize and reproduce its design. And that design has to look really good, and not architecturally detract from the realms it passes through. And, to be really frank here, I really really really don't trust folks on this server to be able to agree on a good-looking skyrail design. Plus, a good design would be highly likely to be resource-heavy to construct over long distances.
But what really makes my decision on the matter is that the more open nature of a skyrail is incredibly condusive to noob grief. Within a few months, there'll be literally hundreds of 1x1 dirt towers all along it that people have used to try and climb up to it. Within a year, there'll be vast tracts of deforested and mangled terrain as far as the eye can see, abandoned and griefed featureless wood cube houses every 50 blocks, and several times as many dirt towers. In two years, it'll be a freaking mercy if all the land under half the length of it's been strip mined to hell. And that's not even mentioning how tempted nub griefers will be to trash the skyrail itself. It's a big tall long structure that looks important. It'd have to be patrolled constantly and rolled back probably several times a day.
So, yeah, there's my main reasons for favoring a subway.
(My personal suggestion for subway design: start with a basic design to establish travel functionality, but leave space around it to expand to more spacious tunnels and multiple lanes in the future.)