Been thinking more about the moveset. I think there should be one special that combines the Djinn attack and the Djinn summon. Otherwise, his moveset would rely too heavily, IMO, on Djinn-related attacks. Also, having the Djinni on Standby and Recovery would lower Isaac's damage output and/or knockback on his non-Psynergy moves, and having it on Recovery -- since that indicates its summon was used -- would power up his Psynergy. Recovery would last... maybe 10 seconds. For ease of Smash gameplay, the Psynergy boost would last only as long as Recovery, instead of longer as was the case in the games. I envision Isaac to be a very potent character on the ground, and he'd need a decent amount of time to make use of powered-up moves, albeit with the negative effects on his other moves, balancing things. For the Djinn system, he may use one or several Djinn, but only have access to one at a time, similar to Olimar with his Pikmin. Also, I've decided that Ragnarok and Odyssey -- which I think should both be included -- should be assigned to a single special, the latter being the charged version of the former (making it more in line with the GS games).
Lastly, before I write out the moveset, I've decided that the entire GS series should be represented in it (not everything in them, of course), but not in a way that would be impossible for a non-Himi Venus Adept. For example, Isaac should theoretically be able to learn Sand, and he would definitely be able to equip the Slap Gloves. So, let's get started.
Smashes
Up: Gaia. This is similar to Sheik's up smash, with two different hitboxes. The first is inside and directly above Isaac, the visual effect being a beam shooting up from beneath the ground at Isaac's feet. The ground then opens up, closing the first hitbox and opening a wider, lingering, hitbox out to one Isaac-width on either side of Isaac. Not sure which hit would do more damage. For balance purposes, probably the first one, since it's smaller and exists for a shorter time. Knockback in the first hitbox would be more extreme, as well.
Side: I decided that my moveset was lacking in plants, so I replaced Ragnarok with Thorn. It grows out of the ground at a shallow angle, hitting the opponent sideways and upwards, but at a sub-45-degree trajectory. I'm not very happy with this selection, as it's not well-suited to be a side smash, but I think Isaac should have at least one foliage-based move.
Down: Quake. Uncharged, it trips the enemy and does a halfway-decent amount of damage for a smash. Charged, it lifts the enemy into the air next to Isaac, then hits them again from there, higher (think of the animations for the stronger Quake attacks in GS).
Specials
Neutral: A tap produces Ragnarok right in front of Isaac (the animation would not be as big as in GS), while holding the button initiates Odyssey. Ragnarok spikes down and to the side at the tip of the blade. When the button is held, two small swords pierce the enemy one after the other, followed by a large sword slamming into the opponent (the animation overlayed on Isaac's character model) along with Isaac lunging forward with his sword. The Odyssey animation would be interruptible at any point by the player (since the button is held), giving this move some combo-starter/mind-game potential. If performed all the way through, its power and knockback would be similar to that of Ganondorf's Warlock Punch.
Up: Megiddo! Isaac leaps into the air and, if he doesn't grab the ledge, slams a meteor down at a steep angle.
Side: Move/Grip. A single press produces Move, which travels a certain distance before disappearing. If the player presses the button again at any time during the Move animation, Grip will initiate. It holds the enemy in place and flings Isaac toward it with sword drawn for a quick strike.
Down: Djinn attack. Whatever Djinni Isaac has, he uses it with this move. It then goes to Standby, making Isaac lighter and his physical attacks weaker. All the while, he's looking for an opportunity to use his level 1 Venus summon, which is decently powerful. Hitting down-b a second time resets the Djinni, returning Isaac's stats to normal, while holding it briefly performs the summon. After the summon, Isaac is still lighter and weaker than usual, but his Psynergy attacks receive a damage and knockback boost for, say, 10 seconds. After that time is up, the Djinni resets, along with Isaac's stats. If more than one Djinni is in the game, the reset cycles to the next Djinni, instead.
Grab: Catch. Range is similar to Link's hookshot or Samus's grapple beam. Has a noticeably different animation to Move.
Pummel: Slap. The Catch hand holds the enemy while Isaac uses Slap on it. Pretty powerful pummel.
Throws
Up: Lift. More of a violent motion than in GS. "Toss" would be a better name for what it does. Still, not very powerful.
Forward: Force. Bam! Pow! Ow! A single, short-ranged hit that sends the enemy sideways.
Backward: Carry. Another "Toss" move, but going behind Isaac. Not very powerful.
Down: Pound. No explanation needed.
Evasion
Air dodge: Cloak. You can still see a dashed outline of Isaac.
Spot dodge: Cloak. Same.
Forward roll: Sand. Faster than in GS, obviously.
Backward roll: Sand. Same.
Tilt, aerial, and dash attacks: His sword, what else? The dash attack animation would look like his normal attack animation in GS, so would be nearly identical to Link's. His sword attacks may not be very powerful taken as a whole, given the strength of the rest of his moveset. They wouldn't be as weak as Robin's non-Levin Sword strikes, however.
Final Smash: Judgment. Making this dependent on Isaac's Djinn status would make things too difficult for him, so I propose that the Judgment summon consist of four random Venus Djinn appearing and summoning the Judgment creature together.
Note: A critical hit sword strike would make for a good side smash, supposing that Thorn should be replaced or moved.