My mistake. I remembered FE Awakening released in 2012/2013. Even so, a release window of something like 2012 could have helped the game wonders. It would both A) Give the devs a lot of time to polish the game and give it the improvements it needed and B) Make it timely enough to be in Smash 4. Would also be in that sweetspot for games that did really well at that time like KI Uprising. It's critical reception would still be "ehh" but at least it doesn't send the series to purgatory for a decade.
Either way, it didn't need to be on the DS really.
2012 was just on the cusp on "timely for Smash" since the project plan went into effect that year, so I'm not sure it really changes much.
Keep in mind, here's the Smash newcomer slate:
Villager - Animal Crossing City Folk (and AC in general)- 2000-2008
Mega Man - Mega Man 10 (and in general) - 1980s-2010
Wii Fit Trainer - Wii Fit - 2008
Rosalina - Super Mario Galaxy - 2007
Little Mac - Punch-Out - 2009
Greninja - Pokemon XY - 2013
Mii Fighters - Wii - 2006
Palutena/Dark Pit - Kid Icarus Uprising - 2012
Pac-Man - Just sort of Pac-Man in general
Lucina/Robin - Fire Emblem Awakening - 2012-2013
Shulk - Xenoblade Chronicles - 2010
Bowser Jr. - Super Mario Sunshine forward - 2002
Duck Hunt - Duck Hunt - Retro from 1984
Basically anything from the Brawl project plan (2005) to the creation of the Smash 4 project plan (2012) was fair game since that was the focus for base Smash 4's roster, so Golden Sun Dark Dawn releasing in 2012 wouldn't have really put it in any better of a position in terms of leveraging Isaac for Smash honestly. It was already in the ideal window for inclusion in Smash 4 and in a different world where Dark Dawn was better and sold better, he might have been in over Shulk or someone else here, but then Dark Dawn just absolutely cratered. It was just really bad timing for Golden Sun to do so poorly since it might have had a real shot for Smash 4 otherwise.
I still don't think a 2012 3DS release changes all that much or that the 2010 DS release was the issue (The DS had an install base of well over 100 million at that point, it always made sense to release the game on the system). It was the middling quality, lack of advertising, and passage of time without Golden Sun that really hurt it. Awakening, Uprising, and New Leaf all exploded in that 2012-2013 period more specifically because they were top quality titles that went out of their way to pick up players new and old with rich gameplay experiences. I'd say they all helped the 3DS more than the 3DS helped them. Dark Dawn would have needed to have been a similarly large step up in quality to have this big "Golden Sun" moment.