Here's a ROOOOUGH sample moveset. I have put thought into it in the past, but it's been so long since I played the first, and I never experienced the second firsthand. But this will get the ball rolling. I don't have a COMPLETE set yet either.
A Down Smash: Punji Strike (Bamboo spears shoot up from below on both sides of him)
A Up Smash: Ray (Magnetic storm focused above his head)
Air Neutral: Tornado (Wind slices around him)
Air Down: Nova (Creates an explosion below him)
Air Up: Prism (Ice crystal attack)
B Up: Glacier OR Eruption (Rides up either on a burst of lava, or an ice pillar bursting upward)
B Smash: Planet Diver (Rushes forward while encompassed in flame, like a meteor)
B Down: Psyenergy - This one is a little more abstract to describe... Remember how he has the giant psyenergy hand in brawl that pushes you? The hand is used for a large number of Psyenergy skills in the games, as I recall, just that different actions had different names, for example, Force was when the hand shot out and knocked into something as a fist. Here's what I propose: Down B activates the hand, making it appear in front of him with the fingers open. While active, Isaac can't move, getting hit enough to flinch will deactivate the hand, and maybe a dash can cancel it to. Also, the "active" state of the hand isn't long, picture it like an FE counter or Peach's Toad. Basically, the action of the hand will depend on the joystick motions in conjunction with the B button, which makes the hand react when pressed again. To balance some of the actions I'm listing, this can only be performed while on the ground.
Psyenergy Active Commands:
None: Hand will catch objects or trap incoming enemies and squeeze them once for damage.
B Neutral: Hand will rest in space as an undamaging wall. Only lasts a short while and using Psyenergy again either makes it disappear, or you can't use Psyenergy again until it disappears (This function seems like it might be imbalanced though by being able to make walls)
B tilt/Smash: Hand becomes a fist and flies forward. Speed of travel would be determined by the power of the joystick press. Doesn't travel far.
B Up: Hand snatches at the air above Isaac. If it catches a player, it basically throws them down like a suplex kind of move.
B Down: Smashes the ground with a fist or open palm for DK style Down B-age OR Dijinni Change (See last part of post)
Final Smash Suggestions:
1. "Giant Sword Attack" : A giant sword falls from the sky, either diagonally down or from straight up. There are a lot of magic attacks where swords fall from the sky in GS, lots to choose from
2. "Summon Attack" : GS also has a crapload of summons. The two most powerful ones that I associate with Isaac because of his Venus affiliation is Judgement and Catastrophe(?). Basically, a big armored angel-god-knight thing fires down a blast or a beam from straight up
I personally feel the best way for him to work is have representation of all four elemental types in his attacks. HOWEVER, I did think up one variation , either through taunting or through the other Down B Down B function I had up there, where he SWITCHED dijinni. The result changes the aesthetic feel of his attacks (for example, Punji Strike suddenly becomes shards of ice shooting up out of the ground), and MAYBE side effects. Fire could leave burning, and ice could freeze, but the imbalance with that is that the other two types don't have an associated status ailment.. maybe lightning could be really fast, light attacks, and earth very slow. -Shrugs-
Anyway, that's a place to start.
Also, here's a GameFAQs document from Golden Sun II listing and describing the attacks. The only trouble is that there is no video to showcase what it looks like, but it'll still help I think. Also most of the really good attacks were brought back, and most have also had additional, more powerful versions added on to them, one example being Ragnarok (the sword from the sky attack) and Odyssey (the stronger version).