In an interview with Nintendo Gamer, Hiroyuki Takahashi said that if enough users ask for a new Golden Sun, it might just happen:
A big reason for us making RPGs comes from the requests from all the people who have enjoyed our RPGs in the past. Perhaps if there are enough Nintendo users asking for another game in the Golden Sun series, then this will naturally lead to the development of such a game.
Don't expect a rush job, though: Takahashi has asked for "a bit of time":
Speaking personally from the perspective of the story, I think that honestly it may not be so likely because Golden Sun really requires a full effort to be put in. But of course, if there are enough people saying that we really must create another game, then we may just have to listen to them. Still, you would need to give me a bit of time to work on ideas for the story before we could release a fourth game in the series.