Give my latest Waluigi vs. Isaac promotion post a read if you haven't, because I'm going to expand upon my thoughts.
The trouble with Isaac is that Nintendo likely doesn't know how much people like Golden Sun and/or Isaac as a character. That's because I feel as if Golden Sun fans don't talk loud enough.
Nintendo has been shown to listen more often than not (at the very least they acknowledge the popularity of something). Golden Sun fans haven't really shown up in droves to demand anything I feel. Their last chance was Dark Dawn, and they didn't really prove to Nintendo that Golden Sun needed to be a thing back then. Regardless of Dark Dawn's quality to fans, to problem is that money still talks. When you have a more niche game franchise not selling well, that just tells Nintendo to not bother. Unfortunately, the same thing likely happened to Chibi-Robo. Whereas let's looks at Fire Emblem:
Fire Emblem: Awakening was going to be the last game in the series because sales for the series were on the decline. Regardless whether or not Awakening was going to go down as a fan favorite or not, if Awakening didn't sell, Fire Emblem would be no more. Luckily, it did. It proved to Nintendo that the series was successful. And because of that, they tried more games. Fates didn't sell the greatest, and Shadows of Valentia sold a bit better, but not close to Awakening levels. To Nintendo, this doesn't tell them that the series just doesn't matter too much, but that there is a style people may favor (they probably realize that more than ever with Three Houses). Unfortunately, if games in a more niche franchise keep selling less and less, the series just isn't going to cut the mustard in Nintendo's eyes.
All in all, I think Golden Sun fans need to speak up more. I would wager a bet that Shadow fans had more of an outcry than Isaac fans. None of what I've said here is ANYTHING demeaning towards Golden Sun and Isaac fans, I'm just saying that if they want to be recognized that they need to speak up more. Take Xenoblade Chronicles fans, because of them, the game was brought to the west and is now one of Nintendo's biggest RPG franchises that is continuing to steadily grow. Another niche franchise being the Mother/EarthBound games aren't that well known too. But you know what, the fans are SO vocal that Nintendo definitely knows of their existence (I mean Reggie talked about Mother 3 God knows how many times due to fans). Do you see what I mean? Metroid is in a similar position as well; the series doesn't sell the best, but because the fans are so vocal, Nintendo knows a lot of people care about the franchise. I just don't think Nintendo knows how popular Golden Sun is, so why would they push for Isaac to be an Assist Trophy when Waluigi is... well, I explained it in my previous post.
Basically, declining sales PLUS no major fan outcry equals a franchise not being on Nintendo's radar.