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Obviouslly excluding the Sinnoh region's honey trees, which of these two are, overall, harder to encounter (taking Pokémon XY as a reference)?
Combee Flabébé

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In which game?
If I would pick a specific game, it would be XY since it is the only game where both of them can be obtained without trading any of them from other game
You may want to edit that into the question.

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The chance of a Shiny female Combee is about 0.0000310251%. The chance of a Shiny White Flower Flabebe is about 0.0000024414%, so Shiny White Flower Flabebe is rarer.

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Are the numbers percentages?
Yes. (filler)