In fact my favourite possibility for Isaac moveset is making use of Djinns and Classes... Isaac would change stats in the middle of the battle in a system similar to the game.
Sol Blade or Gaia Blade. But i would like to see a good redesign of the Sol Blade, i mean Dark Dawn design wasnt bad and in fact pointed in the good direction (Golden, a shape that differences Sol Blade from the common sword) but i think that it needs to be more "Legendary" i dont know what it is but it needs to be more than just a big and Golden Sword, maybe silvery runes or tribals, i dont know...
In my opinion the best place of Golden Sun to make a stage is:
Elemental Star Chamber, While only appears in one game, it have a real importance in the plot of the series. Is the beginning of the action, the trigger that causes the Odyssey of Isaac. And i feel that Elemental Star Chamber represents better than the Lighthouses the aesthetics of Golden Sun. Golden Sun animations makes a heavy use of particles, light... And thats is exactly what Elemental Star Chamber does have. orbs of light floating with grace in the air, the soft light flickering of the elemental stars, the light emanating from the portal and the calmed movement of the water...
Combine that with this:
I can imagine that the main part of the stage would be area around the portal, in the right side we could reach an smaller area that have the venus star statue (just a decoration) in the left side another area similar in size to the portal area, Connecting the 3 areas there would be Pillars that would emerge and submerge randomly and water...
But wait... We can not forget the other face of the alchemy...
This stage could eventually suffer a transformation,
The statues would lose the particular bright that they have, one by one. When the last statue is turned off, the MT Aleph erupts. The stage could have periods of vibration, dust and rocks falling from the ceiling, the water disappears and is replaced by big cracks that emane high temperature materials or even with lava, additionally it could show the awakening of the Djinns (more of the effects of Golden Sun) and the Wise One in the background using his power in order to contain the eruption.