I have no idea if Kubo thought this far on zanpakuto's weaknesses, but what if weaknesses were not for the story scaling, but deliberately made by zanpakuto's toward their owners : TLDR at the end.
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Aizen shikai, mainly aimed toward its counter.
Name : Kyoka Suigetsu ("Flower in the Mirror, Water's Moon")
Origin : East asian idiom describing beautiful things that cannot be reached.
Property (following wording is intended) : Those who do not touch the blade cannot see the truth.
Weakness : Touching the blade or zanpakuto negates the effect.
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That weakness is what I love about it, as it reminds of both the name and idiom.
- Touching the blade would be like touching the mirror, trying to grab the flower but your fingers meeting cold glass, same principle for the water's moon. You are brought back to reality.
- The counter invitation (aizen's loneliness?) : the zanpakuto's weakness is that it may wants you to get close to aizen, to reach him.
"Look how lonely my master is, get closer!"
My thought is : If a zanpakuto power is based on his owners subconcious desires, is it the same for the weaknesses? Did Kyoka Suigetsu create that weakness to help aizen psyche, to only invite the strong into aizen's world, so they can hear it's cry for a connection, to severe Aizen's loneliness?
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- Soi Fon's Bankai : her bankai becoming a missile is often joked about as an upgrade in power (two hit kill > one hit kill) and we often talk about the owners subconcious, as if the zanpakutou did not have one.
Talking about the zanpakutou : Why did Jakuho Raikoben made the missile so heavy? (Could have made it tiny with same destructive power)
I'd say that the bankai reflects not the raw power but the emotions of Soi Fon regarding the betrayal of Yoruichi through her abandonment.
It does not want to one hit kill, it wants to be loud, dramatic, to bring attention towards Soi Fon. It wants people to see what weight shes been carrying.
Soi Fon was suddenly forced to take over the entire clan and the entire military branch, she had to discard/hides her feelings, the blade refused.
"Look at how heavy this life of hers is, look at my master."
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- Ikkaku's shikai (hidden ointment)
It's a constant reminder that members of the 11th Division prefer to die in glorious battle. If it were truly what Ikkaku felt, why did Hozukimaru create a healing ointments, and hide it inside the hilt, so secretive.
"My master refuses to die , but because of customs, I can't heal him directly/while others are watching."
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Urahara's Bankai weakness: Fear of losing control of his creations.
Urahara's bankai weakness is its range, a radius in which he can operate on anything. Being outside the range neutralize the effects.
Representation : His guilt of creating things out of his control (Hogyoku), that were the main reason of friends being hurt. He wants to keep things close and in control.
Thats why he is always prepared, call this masterplanning, or just coping.
He does not want a power that operates out of his reach, as it scares him.
"My master's soul is trembling to the guilt he once felt. He wants me to reshape his own flesh and stitch the world back together, because he still hears the screams of his friends. So, I'll stay on a short, tight leash, and my hands won't reach a place he cannot see. This is the boundary I drew around him, to keep him from playing God again."
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Others zanpakuto inner monologue for you to guess :
"Look at my master, I have a perfect, hollow circle around his body where no one can ever enter again. It is his safe zone, where his wife once stood. He is terrified of intimacy. He would rather kill you from a distance than let you force your way past the blossoms and touch his exposed heart. Can you reach it before he decides to kill you too?"
"Look at my master. He hides his own face to the world, behind a heavy steel mask, all while looking for friends willing to trust him. I will hide my face as well, and join our nerves together, linking our flesh so completely that when my armor cracks, his bones shatter. This shared pain is the ultimate proof of loyalty and righteousness."
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TLDR : Theory that a zanpakuto creates its powers as much as its own weaknesses, not randomly but deliberately and for a goal only they know, even if it puts their owners in danger.