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Was Pikachu temporarily under the effects of R when he used Thunderbolt on Roger's Noivern in the clock tower? The game seems to imply he was, but for all we know, his claim not to remember it could just be him doing his usual "get people to brag on him" shtick.
I thought it was Heroic Willpower that was the cause of Pikachu using Thunderbolt, as its been well established by the anime that for regular Pokemon, learning to talk the human language comes at the cost of being able to use Pokemon moves. It would also make more narrative sense.
Why was Weak, but Skilled taken out? As he's more of a detective than a battler, it would seem proper to describe Detective Pikachu as this.
AFAIK Weak, but Skilled is more about the character's battle prowess and not his other skills (i.e. s/he's weak physically / does not have muscles and / or Super Strength but is still able to royally kick your ass thanks to Kung-Fu or Combat Pragmatism or whatever), and so far we don't exactly know if this applies to Detective Pikachu.
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