Since Star Wars Rebels is set between Revenge of the Sith and A New Hope, it makes sense that Darth Vader could pop up from time to time. And James Earl Jones will again loan his baritone to Vader in an extended version of the pilot episode.
Deadline is reporting that Star Wars Rebels: Spark Of Rebellion, the show's hour-long pilot movie re-airs on ABC on October 26 at 7PM, Jones will make a vocal cameo. Vader wasn't in the pilot when it was released on VOD and premiered on Disney XD, but the ABC broadcast will have an additional scene, one between Vader and the Inquisitor. According to series creator and executive producer Dave Filoni, the scene will offer some insight into the character of the Inquisitor, but I imagine it won't be the last we see of Vader.