Without asking too much, this is how I'd like to see Golden Sun represented in SSB4.
Isaac is the playable character. He's got a solid, Venus-centric moveset that doesn't rely on gimmicks. I'll be fine with whatever it takes to get Isaac on the roster, but I'd prefer a more straightforward moveset than one that relies heavily on gimmicks.
Felix, Matthew and adult Isaac would all work as costumes, but I'd be fine if Isaac only had recolors for his alternate appearances.
He'd be on the default roster in the 3DS version and unlockable on the Wii U version, since he is a handheld character. The Smash games usually have multiple unlock methods, but it'd be neat if one of the ways to unlock Isaac involved beating Master Hand or Crazy Hand.
Felix would be the assist trophy, acting similarly to Isaac in Brawl.
Venus Lighthouse would be the Wii U stage and Craggy Peak Ruins (the place with Zodiac puzzles) would be the 3DS stage. I'd also be happy with Sol Sanctum, Elemental Star Chamber, Belinsk Opera House or Apollo Sanctum as alternate 3DS stages.
The living statues would be enemies in Smash Run. Djinn as enemies in Smash Run would also be cool.
Bramble seeds are an item.
Golden Sun has a number of great music tracks, but Venus Lighthouse better be in there in some form.
There will at least be trophies of the main GS1 characters: Isaac, Garet, Ivan, Mia, Saturos and Menardi. Some of the other major characters (e.g. Alex) will at least appear as stickers).
That said, I'll take whatever gets Golden Sun on the roster. Felix over Isaac because Lost Age is secretly Sakurai's favorite game? Sure. Playable Matthew with Adult Isaac reprising his assist trophy role? Fine with me. Playable Himi and nothing else? Go for it.