Isaac and his son Matthew would represent the Golden Sun series as a whole in Super Smash Bros. so it's important to convey trough them what sets it appart from other series.
In Golden Sun's case, what sets is apart is the use of Utility Psynergy to solve puzzles in the overworld and the Battle System that is interlinked with the unique Djinn and Summon systems.
Due to that, the following moveset tries to incorporate as many of those concepts as possible, but mostly focuses on the various iconic Utility Psynergy that involves hands and the six Secondary Commands used to Fight in battle.
The Djinn and Summon systems are extremelly complex, but I think I managed to do them justice while also reflecting the fact that every Adept can use Psynergy from all four elements and not only the element they are affiliated with.
Since Isaac and Matthew are so similar, the moveset was built upon powers that they get in their respective games and that both would logically be able to use in-game if they were playable in each other's games.

Explanation

Isaac uses the power of the Teleport Lapis to Teleport into battle.

Isaac carries the Sol Blade sideways like Matthew does in Dark Dawn.

Isaac replicates his Golden Sun iddle poses, which mostly consist of him looking around.

Isaac uses the power of the Cloak Ball to Cloak himself in the shadows and avoid the opponent's attack.

Isaac uses the power of the Hover Jade to manipulate gravity allowing him to step in the air during his second Jump and then Hover after it to slightly extend his air time. (works somewhat like Yoshi's Flutter Kick but horizontally, as if Isaac was walking on the air)

Isaac puts up a Psynergy barrier that looks like a regular Smash shield but is blue in color.

Isaac hits the opponent with a regular swing of his Sol Blade.

Isaac hits the opponents with a regular swing of his Sol Blade. Alternatively this move could be based on Sol Blade's Centurion unleash.

Isaac hits the opponents with a regular swing of his Sol Blade. Alternatively this move could be based on Sol Blade's Purgatory unleash.

Isaac hits the opponents with a regular swing of his Sol Blade. Alternatively this move could be based on Sol Blade's Radiant Fire unleash.

Isaac jumps forward and hits the opponent from above with a swing of his Sol Blade that "results in a Critical Hit". (works like Link's Dash Attack, but maybe slower due to him wielding a two-handed long sword)

Isaac hits the opponent with the Ragnarok Psynergy. Since the sword moves diagonally it can Meteor Smash opponents hanging on ledges when it hits the ground.

Isaac hits the opponent with the Planet Diver Psynergy. Has Flame effect.

Isaac hits the opponent with the Astral Blast Psynergy.

Isaac hits the opponent with the Cutting Edge Psynergy. Has Slash effect.

Isaac hits the opponent with the Gaia Psynergy. (works like Palutena's Up Smash, but is wider in length and shorter in height)

Isaac hits the opponent with the Starburst Psynergy. Has high Knockback.

Isaac hits the opponent with the Haunt Psynergy.

Isaac hits the opponent with the Thorn Psynergy.

Isaac hits the opponent with the Quake Psynergy.

Isaac hits the opponent with the Spire Psynergy. Can Meteor Smash airborn opponents if it catches them below the stone spire.

Isaac hits the opponent with the Sleep Psynergy. Has Sleep effect.

Isaac hits the opponent with the Break Psynergy.

Isaac uses an Oil Drop surrounding himself in Flare Storm Psynergy that burns opponents. Has Flame effect.

Note: Some of the other Utility Psynergy coming from equipable items could be used for Aerial Moves instead.

Isaac uses a Weasel's Claw hitting opponents with Sonic Slash Psynergy. Has Slash effect.

Utility Psynergy Items

Isaac uses a Crystal Powder hitting opponents with Hail Prism Psynergy. Has Freezing effect.

Isaac uses a Bramble Seed hitting opponents with Nettle Spynergy.

Isaac drops a Smoke Bomb on his opponent. Has Stun effect.

Isaac drops a Sleep Bomb on his opponent. Has Sleep effect.

Isaac grabs a ledge using the Grip Psynergy. If it catches an opponent, it will squeeze them once using Grind Psynergy.

Isaac grabs an opponent using the Grip Psynergy produced by the Grip Crystal.

Isaac lifts an opponent in the air using the Lift Psynergy produced by the Lifting Gem. Maybe he could be able to carry opponents around after grabbing them, much like Donkey Kong, by using the Carry Psynergy?

Isaac picks up an item using the Catch Psynergy produced by the Catch Beads.

Isaac carries said item using the Carry Psynergy produced by the Carry Stone.

Isaac uses the power of the Grindstone to grind opponents with its Grind Psyngery. It would be visually similar to how Master Hand squeezes the player character.

Isaac uses the power of the Orb of Force to hit opponents forwards with the Force Psynergy. Has high Knockback?

Isaac uses the power of the Slap Glove to hit opponents backwards with the Slap Psynergy.

Isaac uses the power of the Scoop Gem to hit opponents upwards with the Scoop Psynergy.

Isaac uses the power of the Pound Cube to hit opponents downwards with the Pound Psynergy. Has Bury effect?

Isaac uses the power of the Lash Pebble as he gets back up, tripping opponents surrounding him with a rope produced by Lash Psynergy. Alternatively, he could use the Growth Psynergy to similar effect, since Matthew can use it at all times.

Isaac hits the opponent with a regular swing of his Sol Blade.

Isaac will use the Move Psynergy, shooting an hand that will travel a short distance forward, blocking projectiles and knocking back opponents without damaging them. This would be a smaller version of his Assist Trophy in Brawl.

Isaac's Brawl Assist Trophy

Isaac can unleash his Set Djinni to attack the opponent, which will then put it in Standby mode. Each element uses the Djinni listed to the right, to make things less complicated and more predictable.
The Djinni can then be restored to Set mode again by using Set Djinni, which won't cycle to the next Djinni in the sequence if used under these circumstances.
While the Djinni is in Standby mode, Isaac defaults to the Squire class when using his Smash moves.

Using the Side Special while a Djinni is in Standby mode will then unleash a Summon of the Djinni's respective element.
The Djinni will then enter Recovery mode for a short period of time, meaning Isaac can't use Set Djinni or Djinni Unleash until that time period is over.
In the meantime, Isaac defaults to the Squire class when using his Smash moves.

Isaac uses the Retreat Psynergy to rematerialize as close as possible towards the stage.

Isaac puts the current Djinni in Standby mode and Sets a new Djinni, changing classes.
The Djinn rotate in this elemental order [Venus > Mars > Jupiter > Mercury] and the Venus Djinni is always Set by default at the start of the match.
Isaac's Smash Moves and Stats change to fit each class, which rotate with the respective Djinn like this [Squire > Brute > Apprentice > Crusader].
(Squire = Balance, Brute = Attack, Apprentice = Agility, and Crusader = Defense).
If no Djinni is Set, Isaac will default to the Squire class and his Stats will be slightly weaker since no Djinni is boosting them.
The Djinn will also visibly accompany Isaac, or maybe make him glow in their element's color, so players can tell which Djinni is currently Set to him.

Isaac hits his opponents with the Sol Blade's ultimate unleash, Megiddo.

Isaac flips a Lucky Medal towards the sky and then catches it with his hand as it falls back down.

Isaac drinks a sip of Herme's Water.

Isaac holds the Sol Blade above his head as energy flows around him. The color of the energy would change according to the currently Set Djinni.

Isaac says something and then dematerializes into Psynergy particles that leave the screen.

Isaac raises his arm, making a V-Sign pose.

The four Djinn in Isaac's possession play around him while forming a circle, making him laugh heartily.