No offense but I'm not really sure what you're saying exactly...
I'd imagine that the female protagionists that are more in support roles, like Orihime from Bleach for example, are probably more popular in Japan due to sex appeal and whether fanboys can purchase merchandise. But then again, I'm not Japanese, so I have no clue, other than sex sells.
I know in the West, characters like Ryuko and Satsuki and even Mikasa from AoT are popular because they kick ass.
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