By ship
Even cheaper and more scenic, but available for the northern crossing only, are ferries that cross from Akashi to Iwaya for a mere ¥320 on the slow boat all of 24 minutes (http://www.taco-ferry.com...) or ¥450 for the fast boat a zippy 13 minutes via the Jenova Line (http://www.jenova-line.co...) located south of JR Akashi Station.
By train
There are no direct train services to Awaji Island. Highway buses run directly from major train stations, such as Shin-Kobe on the shinkansen ¥1800 to Sumoto, and Osaka and Sannomiya stations on the regular JR line ¥2300 and ¥1800 to Sumoto, respectively. From Shin-Osaka station you must either take a local train one stop to Osaka station, or remain on the shinkansen to Shin-Kobe, to transfer to the bus.
Buses to Awaji Island are not valid with the Japan Rail Pass. Tickets can be purchased from "Midori-no-Madoguchi" locations at each station.