The companies work for Nintendo, so Nintendo really just needs to go and ask them. It is not like they would decline, it advertises their games.
Thus more franchises can be repped.
That's not how corporations and business works. There is actually a ton of legal issues that need to be sorted out before 2nd party characters are added. You're still borrowing IP, even if they work for you, you simply can't go up to them and say, "hey, we're taking your **** since you work for us, you cool with that?"
Technically speaking Golden Sun is not dead. The most recent game in the series left off with a cliffhanger, so it still has leg room to expand further. The problem is that there doesn't seem to be a motivation to expand on it at the moment. Though unlike how some people think here, that is not really a huge loss considering Golden Sun is very uninteresting.
Besides, Golden Sun is only partially owned by Nintendo. Going by theories, characters from second party franchises won't be included on the roster to avoid any form of copyright complications.
Yeah, I guess. Thing is, the franchise has little to no light left in it, and honestly it isn't THAT good nor well known. Meanwhile Xenoblade is hailed as the best RPG of this generation in several circles (whether or not I agree with that statement is something else), and is generally more well known than GS was back then among gamers.
GS was VERY niche back in the day, the internet was still relatively less connected, and news got around much slower. Only popular games saw the light of day for the most part, as word of mouth was what carried info, and review sites like IGN and Gamespot was still largely trustworthy.
Nowadays things are much different. The internet is much more connected, review sites can't be trusted and word of mouth dominates. Games find it much more easy to get advertised as viral news and information travel across the net in mere minutes. Perhaps if Xenoblade was born in the same era of GS it would have remained as niche and undiscovered as GS, but the thing is Xenoblade was born in JUST the right time for it to launch as a very well know RPG on the Wii. I would honestly put it on the same scale as Bayonetta in terms of notoriety.