Wasn't there some kind of Pokemon canon split done to separate the canons of the anime, manga, & games from one another?
That said, Ditto copies genetic/cellular structure. It's not stated to be molecular level, AFAIK.
& its transformation is known to be fallible & varying.
| Emerald | A Ditto rearranges its cell structure to transform itself. However, if it tries to change based on its memory, it will get details wrong. |
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| Sun | It can reorganize its cells to make itself into a duplicate of anything it sees. The quality of the duplicate depends on the individual. |
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| Ultra Sun | While it can transform into anything, each Ditto apparently has its own strengths and weaknesses when it comes to transformations. |
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& the info about the Transformations seem to imply it maintain its own mind, which would imply Ditto's own flaws:
| Scarlet | Its transformation ability is perfect. However, if made to laugh, it can’t maintain its disguise. |
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| Gold | It can transform into anything. When it sleeps, it changes into a stone to avoid being attacked. |
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| Sword | It can reconstitute its entire cellular structure to change into what it sees, but it returns to normal when it relaxes. |
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If it were as thoughtless as an actual stone, I doubt it'd wake up, & if stuff like personality or intelligence carried over, a partially failing disguise during amusement might mean partial loss of the form's mental add-ons causes a joke to suddenly cease being understood & thus, cease being funny to Ditto, but that doesn't seem like it's what happens.
Similar for Ditto reverting upon relaxing.
& it's not like Pokemon completely shows adherence to how the mind is a plaything of the body, given magic, psychic powers & the undead are things.
How is it copying Magic Guard, or the Fairy typing of a Pokemon affected by Magic Powder? The Plasma-based body of Rotom, the incorporeal body of many ghost-types? Vaporeon has cell composition similar to water molecules, Water makes up 80% of Manaphy's body, Sinistea is possessing a teacup, Sinistcha is matcha tea, Slugma is moving magma, Magnemite is floating metal magnets.
Vanillite is an icicle that didn't want to melt in the morning sun!
| Emerald | A Ditto rearranges its cell structure to transform itself. However, if it tries to change based on its memory, it will get details wrong. |
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| LeafGreen | Capable of copying an opponent's genetic code to instantly transform itself into a duplicate of the enemy. |
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For those, among other Pokemon:
WHAT GENETICS?
Copying those shouldn't be plausible if we adhere to real world science about genetics & cells as things like water, teacups, ghosts, magic, magnets & frozen water do not have DNA, genes nor cells!
So what do we do know points to Ditto still maintaining some of its own mental issues (Which may vary by individual, apparently.) like being unable to maintain its transformation if it laughs, returning to normal when it relaxes, not literally losing its mind when it turns into a stone to sleep in peace instead of pieces, & Pokemon not being entirely reliable about what has genetics.
If we're to assume it copies Intelligence we need feats. To its credit it copies moves, but we don't know how skillfully.
Does every martial artist remember the ideal motions for all their techniques every day of their lives?
Every alchemist remember every formula in exactitude?
Every diplomat all the customs for every scenario?
If you copied someone's brain on a given day, I'm skeptic they'd have perfect knowledge of all the things they can do at the time, even if it's their profession they train for. People screw up & I'm skeptic Pokemon are so perfect there either, if you'll forgive this somewhat argument from incredulity.
IMHO, Ditto's entries lean more towards it maintaining its mental flaws, the matter about relaxing suggests being Ditto is less Stamina-exerting than being Transformed, & Level is game mechanics, so we defer to game mechanics.
& because of the canon split, stuff about Ditto in the games would have to be argued against using stuff from the games.
What in the games contradict the user maintaining its own HP & Level, or Transform only granting only 5 PP per move per instance of Transforming?
What are the feats in favor of Ditto copying Stamina & Intelligence despite what info we have pointing at least slightly otherwise, especially when Pokemon's adherence to genetics/cells, which are the basis of Ditto's Transformations, is sometimes dubious?