not to spoil the idea but this just came to mind
http://xkcd.com/1205/if there is one ride to spawntown per day (and i think one per week is more accurate)
the distance can be estimated at 1600m (desertopia is 1km, kaeshar a bit farther, aeridani too).
that is 200 m by nether
sprint is a bit over 5m/s, rail is 8m/s
40 seconds vs 25 seconds
15 seconds saved, and probably less because of minecart getting on and off
so it is worth around 2-12 hours (5 hours geometric mean) to build the netherrail and stations and move portals and dig tunnels
else you should just walk
and this assumes blacraft continues at this activity rate for five years