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Power Bow
Again, the Smashwiki's lack of custom move data on Link made it difficult to pinpoint the good custom moves from the bad. Power Bow cannot really be used as a zoning tool due to it's longer charge time and lack of range, with uncharged arrows being almost useless. It is a good KO tool that could insert pressure, but Link's own moveset has enough power as well.
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Farore's Windfall,
Nayru's Rejection
Her customs.... suck. Only two moves in her arsenal overall outweigh their normal variations (see more at the best customs article). Farore's Windfall is bad: it only sends Zelda up, and the fact that it meteor smashes significally hinders it's KO potential. The meteor smash can be used at the side of the stage so the opponent would get spiked, but the move is extremely situational and not worth using. However, Nayru's Rejection is arguably even worse, for it has more startup, has a lower reflection multiplier, and less damage. The move is designed to reverse oppenent's direction like Mario's cape, but the startup, combined with the fact that the move flinches the oppenent, makes it mediocre on doing that. Not worth using at all.
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Skimming Grenade
Sheik's customs are generally good. Skimming Grenade, however, struggles to outweight the strengths of her other two variations. The grenade bounces on the ground away from Sheik with a controllable timed delay before exploding. The explosion deals less damage, but the bounces can deal up to triple the damage of the regular version's hit and pull. You are hardly going to use the bounce's damage anyways (except for maybe specific matchups), so there isn't too much point. According to the in-game description, the move is supposed to adjust damage depending on how long it is out, but it deals the same damage nevertheless. Strange.
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Warlock Thrust,
Dark Vault
While Ganon drastically benefits from customs, two of them does not have strengths that outweigh the default's strengths. With Warlock Thrust, the backfist is faster and produces a large explosion of dark magical energy, giving it more vertical range, transcendent priority, and less ending lag. The explosion, however, is a large sourspot, with Ganondorf's fist being the only sweetspot in the move. As a result, it deals extremely weak knockback that does not KO until past 300%. This, combined with the move still having a large amount of ending lag, makes the move even more unfeasible, making it heavily inferior to his other neutral B variations. Dark Vault does not give a noticeable amount of increased distance, and can only grab during the beginning of either vault, and has no ending uppercut. Has less horizontal distance, the electrocution ends faster but deals drastically less damage and the explosion has less knockback power that KOs at 400% instead. There also is some lag between the two vaults, making it much easier to edge-guard. Dark Fists is a significantly better option so use that instead.
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Piercing Bow,
High-Speed Boomerang
Toon Link has very few customs moves that are overall inferior to his default special moveset. Both of these moves sacrifice some utility (with Piercing Bow having less range and deals noticeably less damage, and High-Speed Boomerang dealing less damage and is tilted only horizontally during its flight and return, which results in its hitbox being consistently smaller than Boomerang's, and having slightly more start up) for the ability to pierce the opponent, with High-Speed Boomerang travelling faster. If customs are allowed in doubles, these two moves would become especially useful there.
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Screw Rush
Samus's customs grant her benefits, and her worst custom moves are not terrible at all. Screw Rush is effectively her worst out of them. It deals more damage and knockback, which grants it better KO potential. However, because it launches opponents horizontally, it only KOs reliably near the edge instead of near the upper blast line. It also covers more horizontal distance, but covers significantly less vertical distance, making it less effective for recovery. Considering that Apex Screw Attack is much more reliable in terms of up B KO moves, it makes this move seem less effective in comparison.
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Shooting Star Flip Kick,
Low Flip,
Impact Kick
As mentioned before: Zero Suit Samus' customs are among the most polarized in the game. New advantages are gained from using them, but each one has a noticeable disadvantage to go alongside them, to the point that some are inferior to her default specials because of their disadvantages outweighing their advantages. Shooting Star Flip Kick and Low Flip have much less utility overall: the former is difficult to hit with, whereas the latter is less reliable for both recovering and KOing. Impact Kick is much slower, which removes its status as a follow-up entirely and often makes it unable to connecting with itself.
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Impact Orbitars
The Pits doesn't entirely have a custom move that is directly inferior the default moveset. Impact Orbitars are offensive variations that generate two semi-spike hitboxes on each side of Pit. They also grant super armor. However, they have a much shorter duration, and are unable to reflect projectiles or block melee attacks. Considering his other variations pushback and projectile reflection, this move seems unwelcoming, although it could an optimal choice against no projectile opponents and isn't the PK Kids (he can use the other two orbitar variations to gimp both of their recoveries).
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Explosive Flame,
Heavenly Light,
Rocket Jump
Palutena gains drastic benefits from customs, and turns into a virtually different character. However, some of her moves is not that good at all. Explosive Flame is a pinpoint explosion that is just as slow as Autoreticle, although its limited range makes it even more difficult to land than Autoreticle, as well as being easily punishable if the opponent is in the middle of her and the explosion. It would've been a potential viable alternative to Autoreticle, if it wasn't for the nerf at 1.1.1. Heavenly Light has very minimal use in singles play because of its inability to KO or even flinch. However, these traits also make it invaluable in Team Attack-based doubles play as a method to supplement Ness, Lucas, Mr. Game & Watch, and Mii Gunner's absorption-based moves. Rocket Jump has a meteor smash hitbox below her in midair and a strong hitbox that notably improves her out of shield game, yet is inferior to both Warp and Jump Glide in every other way.
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Effortless Blade,
Dolphin Jump
Marcina has some customs that isn't truly terrible, but is mediocre overall. Effortless Blade is essentially a poor man's Dancing Blade: it makes the hits easier to link, but only allows forward (red) swings. Since Marcina swings with less vigor, the attack is also much weaker. Dolphin Jump is purely vertical and gains more height, although it can provide more horizontal momentum after the move's conclusion. However, landing lag is significantly increased, and the jump deals no damage, making it easier to intercept.
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Unyielding Blade
He doesn't really have bad custom moves, with Aether Drive being arguably situational. Unyielding Blade is generally situational in that regard. Deals more damage, to the point that when fully charged, it KOs middleweights at 93% while near the edge of Final Destination in the 3DS version. It also grants super armor for the duration of its charge and lunge. However, it is much slower and has less range, which make it virtually unusable for recovery.
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Soaring Elwind,
Distant Nosferatu
Robin's custom are generally mediocre. Soaring Elwind alters the lifting power of each gust. The first hit has less recovery potential and deals less damage, but the second hit has much more recovery potential. But because the first Elwind going less distance makes the move more vulnerable for the tome to run out putting Robin in a bad position. Each gust takes significantly longer to cast, which makes it easier to intercept. Distant Nosferatu grabs opponents farther away instead of at close range, but deals less damage, heals less and is slower. I don't really see the point of using it over Nosferatu, but it be used to surprise unwary opponents.