What I had actually considered was making the Djinn system involve solely Neutral B, and it could be implemented after the fashion of Shulk's new system for choosing his active Monado Art. First of all, tapping B uses a Set Djinni and then puts it into Standby, which removes it from a train of three invulnerable Djinn following Isaac around on the stage. Holding the button, however, allows you to input a direction on the stick that determines what happens next: down gives you the Venus summon; forward, Ramses; and up, Cybele. If you push the stick backwards, instead, you reset the last Djinni used (and to avoid chaos and greater complexity, the Djinn can only be used in one order; also, the first will always be Flint, for series recognition).
Why reset? Because the fewer Djinn Isaac has Set, the more damage he takes from enemies, the less damage his own attacks deal, and his side special degrades to a less powerful Psynergy. However, when Djinn are used for summoning, Isaac will get a temporary boost to the power of whatever Psynergies he has available until the final Djinni in Recovery switches back to Set (with each Djinni taking a set amount of seconds to switch back). The tradeoffs inherent in the Djinn system would certainly need precise tuning to make it feasible for Smash, but it could be done easily enough. And I should note here that none of the three summons mentioned would be overpowered. No, that remains for Judgment. Once Isaac breaks open the Smash Ball, he gains Ground as a fourth Djinni. Pressing B will put Isaac's other three Djinn on Standby and will use Ground, making opponents within a certain area in front of Isaac unable to move, and they will get the KO blow that the center of Judgment's blast will deal. Everyone else will eat the blast wave, though it can be dodged if your reaction time is sufficient.
A feasible variant of the above could be that holding B just summons the strongest Venus summon possible given the number of Djinn you have on Standby. And because of this, there would be no option to reset Djinn. So it would be down to the player's choice (first option), or to easier programming (if ever so slightly) and greater predictability in battle (this option). I would be fine with either one. And in fact, the second option would lend more strategy to matches. It would probably be the preferred path for Sakurai and his team, now that I think about it more.
What would Isaac's other specials be? For starters, I want to address the elephant in the room that is Super Smash Flash 2: while Move and the Psynergy hand are what Isaac is known for in Brawl, and thus in Smash in general, SSF2 gives them too prominent of a role. A giant floating hand and the Golden Sun abilities that can be performed with it almost perfectly correspond to what one would want out of a grab, pummels, and throws. Attack Psynergy, weapon unleashes, and Djinn are too important to be nixed in favor of the hand, as interesting as SSF2's implementation of it is.
Up Special: Megiddo
Obviously it needs to be adapted in the same manner as Ridley has been from previous Smash games to Ultimate. I had this as his recovery move in my last moveset, and nothing has convinced me to abandon it. Isaac leaps high into the air and slashes his sword downward. If B is held until the apex of the jump, a large-ish, flaming chunk of rock forms in the air where the apex will be, and Isaac slams it down diagonally at the ground, which does a pretty good amount of damage. Getting hit by Isaac's sword during the slam causes a diagonal spike along the future trajectory of the rock, causing the opponent to ricochet off the rock and diagonally into the air behind Isaac. Getting hit by his sword when no rock forms will cause a spike in the same initial direction (to the side at a steep downward angle). After the slash/slam, Isaac goes into freefall. This move is risky except when used as a recovery from almost straight beneath the ledge.
Side Special: Odyssey/Ragnarok/Sol Blade's Purgatory/Critical Attack
The identity of this move depends on how many Djinn are Set. If all three, the special will be Odyssey; if two, Ragnarok; if one, Sol Blade's Purgatory; if zero, then a mere critical attack with Isaac's sword. The strength of the move -- and its riskiness -- goes up with the number of Set Djinn. Whereas Odyssey requires time for two small Psynergy swords to pierce the air in front of Isaac before the large Psynergy sword smashes through them, Ragnarok is fairly quick (and its tip spikes diagonally downward at the conclusion of its motion). Getting hit with one of Odyssey's small swords causes a flinch; getting hit with both traps you into getting hit by the large sword. So as not to make Isaac overpowered, the Psynergy swords involved with these moves are much smaller than in the GS games. I'm open to Ragnarok and Purgatory being swapped, since I think the latter might be stronger in Dark Dawn.
Down Special possibilitiy 1: Move
I initially reserved this for resetting Djinn, but since I worked it into the Neutral B "system", this special slot has been freed up for something else. Why not Move, since people seem to want it?
Down Special possibility 2: Growth
As in SSF2, it will immobilize the opponent, though this version would come from the ground instead of from... Isaac's hands.... Does minimal damage and is mainly used to keep someone at bay.
Down Special possibility 3: Spire
When grounded, drops a rock spire on an opponent a few feet in front of Isaac. When used in the air, spires form underfoot that Isaac hops across; works as a horizontal recovery move, supplementing Megiddo's upward motion for getting back to the stage.
Down Special possibility 4: Grip
Only if tether recoveries are NOT in the game, because I would rather have it as a tether recovery. This would do no damage. The hand would go out horizontally and grab someone in front of Isaac, then bring Isaac to them, where he performs a strong slash with his sword.
Tether recovery: Grip (if possible; would free up the down special for one of the other options)
Isaac's other, more "earthy", Venus Psynergy will be used for his tilts and smashes (mostly, anyway) -- or, seeing as this is Smash Bros. and not a dedicated Golden Sun fighting game, I could compromise and have them only as smashes.
Up Smash: Gaia
The ground opens up several feet in front of Isaac and a volley of rocks erupts from the fissure. I'm open to this move happening on both sides of Isaac.
Side Smash: Thorn/Briar (the... "pokey plant" Psynergy, whatever it's called)
Erupts from the ground in a diagonal direction, with consequences for the opponent's trajectory thereafter.
Down Smash: Quake
Columns of earth erupt sinusoidally a few feet in front of Isaac. Has great upward launching potential at the center, but the extremes merely cause tripping.
Grab: Catch (mid-range)
Pummel: Slap (?; with the Slap Glove, of course)
A second hand appears alongside the Catch hand for this.
Up Throw: Lift
Another two-handed move.
Down Throw: Pound (buries opponent)
Forward Throw: Force
Backward Throw: Carry
Another two-handed move. Violently swings opponent behind Isaac at the same distance opponent was grabbed at and lets go.
Standing Hold-A attack: Dark Dawn Sol Blade's Centurion
Similar to Link's Standing Repeat-A attack from Melee.
Running Attack: Dark Dawn Sol Blade's Radiant Fire
Final note: My version of Isaac is a behemoth at mid-range, where most of his specials and smashes occur at, but -- depending on whether or not his Psynergy is also used for tilts -- only mediocre at close-range. Consequently, some of his moves aim at pushing his opponent away from him and into range of his Psynergy and summons. Supposing that his down special is Move, you can see how this might play out.
Edit:
Spot dodge: Cloak
Just your typical character animation, except that he goes completely black during the dodge, possibly with a dashed outline, as in the GS games.
Roll: Sand
Turning into sand and then reforming from it on the other side of your enemy seems rather entertaining.
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