While I do agree that Isaac should be as Isaac as possible, and not just a hodgepodge of Golden Sun references, I do not think that he should be exclusively Venus psynergy. After all, the Djinn and class systems are a big part of Golden Sun and Isaac. Having him use some of the abilities that he would have as an Illusionist, or Ninja, or Dragoon, or what have you, certainly have a place in his move set.
I don’t think an entire class switching mechanic is necessary. In fact, I’d prefer he use Venus attacks for nearly all of his moves. After all, there’s plenty to pull from (Quake, Growth, Briar, Gaia, Ragnarok, Curse, Spire). However, I feel that maybe having him use Cutting Edge as a forward smash, or Flare as an up air, or maybe Astral Blast or even Shuriken as a forward air would be incredibly neat, and really round out the character for me. Because personally, when I play through Golden Sun, Isaac is using Jupiter psynergy almost just as much as Venus Psynergy. And I’m sure that most GS fans have a certain class that Isaac usually sits in that they’d like to see represented.