In the ds's case I really think it's piracy that holds back the sales. The thing with popular franchises like mario and zelda is that they are known by everyone which also brings a great amount of people who actually buy their games(mainly young and old). In golden sun's case the amount of people who know the games are mainly around their 16/20 who might have allready figured out flashcards.
It only gets worse with time when words get spread and DS flashing is the easiest piracy ever. Now the ds life cycle is almost over with 3ds coming out next year, I think a great large amount of people have found the flashcard method.
Sadly the golden sun series might only be bought by those who still didn't figure out flash cards or die hard fans, which isn't a large amount and maybe kind of explains it's failure in sales.
I personally had a flashcard too, but the Antipiracy security in games became pretty drastic and I stopped using mine a year ago. The thing is that new flashcards bypass the securities, but I was never bothered to get a new one.
I bought my golden sun, but I would have still bought it even if I could obtain it by downloading the game. Good games are worth to be bought and I love owning the cases from such special games.
Anyway, Just a little bit of info about the game you'd might like to hear. In this new installment you play with the sons and daughters of the main characters of golden sun 1. All the characters from golden sun 1 are now your parents lol. The script is really nice written and even though the characters from GS1 have gotten old, they still have the same characteristics. Isaac the main character from GS1 now talks and seems to be very knowledgable in this game while garet is more silly than ever lol. Garet for instance, from golden sun 1, is really clunky and hardheaded. But his son is even worse lol. I highly recommend this game to anyone who like JRPG's. Personally I think this game tops most of the console JRPG's.