I just got done reading some topics on the Golden Sun: Dark Dawn message board at GameFAQs and they are really pessimistic about the future of that series. There are a few of them that think the only way to revitalize the series would be if Isaac were to be playable in Smash 4. Other than that a lot of them have pretty much resigned themselves to the fact that the series probably won't get another installment.
Also, throw in that the higher-ups at Golden Sun say that they will do a GS4 if there is enough demand for one, but then later on in the response admit it probably won't happen. The Camelot guy was also saying how difficult it is to write a story for a RPG and how much writing for Dark Dawn drained him, and went on and on about that.
I feel a lot of sympathy for the Isaac supporters, not only are they fighting for a character, they are fighting for a series. Isaac still has a lot of support in the West, however, lately Shulk has started to eat Isaac's lunch here too:
http://www.gamefaqs.com/boards/633202-super-smash-bros-wii-u/64895787?results=1#1
I have not played the Golden Sun games, so I am neutral on Isaac in general though.
This may be a common theme for a lot of Nintendo characters that are being requested for Smash Bros. Inclusion in Smash Bros. means survival for a lot of them.
I'm late to the Isaac and GS discussion, but I'd still like to weigh in. Isaac has been my most wanted character for Smash since pre-Brawl (actually since I first played GS a little after Melee), and I've never deluded myself into thinking that he was ever one of the most likely candidates (during Brawl his series had more prominence but he had better competition, and now his series is in a definite decline), but I agree, the Golden Sun series could very well be over now without some intervening from Smash, which means this might be Isaac's (or Matthew's) last real shot at inclusion. I still think he has a fairly decent shot at inclusion this time around (though not what he had during Brawl's time), along with the fact that, excluding Punch-Out, no new IPs really stand out as incredible likely to be included, giving GS a decent chance, as it is one of the more successful and established IPs left unrepresented. However, I won't deny his chances are slipping pretty rapidly, and in another couple of years he will definitely be outclassed by several other candidates.
Like some others have said, it's not impossible that Camelot will make a Golden Sun 4, but it is (at this point) fairly unlikely. Perhaps if there was more hypothetical support for his series in Japan, where his genre actually still fares fairly well. Of course, that is a double edged sword, as many JRPGs outclass Golden Sun's recent output as well, including Xenoblade. I'd agree that right now his series in indeed on the line with Smash inclusion as one of the only realistic opportunities for it to continue, and even then it's a gamble, Camelot doesn't really need the IP to survive, it has Mario's tennis and golf games which will always bring more success (commercially at least) than a GS game would, which is sadly what is usually boils down to. Even if Isaac (or Matthew) is included in Smash 4, that's no guarantee it'll provide "safety" to his series, though it definitely would help.
As it stands now, this seemingly could be the last real shot a GS character has to be included in Smash (barring any surprise and unlikely non-influenced by Smash fourth game), and even now it's kind of iffy, which is a shame, because the series as a whole is wonderful, and one that could use more attention IMO.
I've come to terms that Isaac is not the fairly likely character choice for Smash 4 that alot of the west seem to think he is, and I'd personally only give his chances at around 50/50 (and some would even give his chances less - which could also be valid).
The only other IP's survival I feel might hinge on Smash inclusion (with a character who has at least decent chances) is Sin & Punishment, but even then I wouldn't be so sure of it's safety, as the whole S&P series has brought less in total than just Dark Dawn. I honestly feel that IPs such as Starfy and Custom Robo could survive without Smash, their future depends more on the choices of their developers, especially as Noise really only has either Custom Robo or creating a new IP, and they are both still decently profitable, at least in Japan.