Since I've been playing through his game, Isaac has a ton of potential. His smash attack could be based on his critical hit animation, and connecting with the hit produces a satisfying crackle sound.
He has access to Venus Djinni, which is fancy terms for "earth magic." Mother Gaia has a hole opening in the ground to have rocks shoot out of it vertically upwards, which can work as an anti-air special not unlike Ivysaur's vBrawl Bullet Seed attack. Isaac can also use lush vines in an attack called Growth when he uses a combination of Venus Djinni and other elemental Djinni, so the vines can be used as a tether or recovery special. Maybe it can be a tether that's unique among others in that, unless you're in the air, it comes out of the ground in front of Isaac rather than Isaac's hand, or something. While he uses a variety of weapons like swords, broadswords, axes, etc. I think just limiting it to a forward smash is ideal, like how Ness and Lucas' signature weapons are only featured in their f-smashes (yo-yos are usable by every party member in EarthBound so it's not really a "signature" weapon for Ness).
Spire is an attack that summons a stalactite of rock to fall on your opponent, which is something else to think about. I have this weird idea where it can be used in Isaac's pummel, but it's a single-hit pummel (the only one in the game, theoretically), instead of rapid / multiple hits like every other fighter. It'd be so strong on its own that it causes a ton of percent to go up, but you automatically let go of your opponent after doing one., meaning his throws shouldn't be chain-grabbable for the sake of balance.
Shin has actually beaten Golden Sun (I'm currently in the middle of Venus Lighthouse), so he can contribute more.