I think it'd be neat to have a console Golden Sun game, and of note, we've got several Pokemon RPG's, Xenoblade (which is more of a hybrid action-based RPG), and no turn-based RPG's yet. Also, Golden Sun was re-released, we should see Golden Sun: The Lost Age soon, and since DS games have been released on Wii U Virtual Console, we may also see a re-release of Golden Sun: Dark Dawn all on the lineup to Golden Sun 4, making the jump from handheld to Wii U.
It could happen, although I think it'd be more likely for Golden Sun 4 to stick to 3DS. Regardless, though, I think Golden Sun 4 is happening soon, and now would be the ideal time to add Isaac to Smash Bros. to promote it. That said, he might be unlockable, because Dark Dawn didn't sell that well and likely isn't currently on the market, so Isaac won't be marketed too well, but he may still be in the game.
So yeah, there's definitely a lot of good things going for Isaac. We just have to see how things play out.