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Correct. Greninja was chosen long before XY were released or Greninja was made public.

Because Greninja was the designated ace Pokemon. Same reason Ash also has a unique Lycanroc now.

Because they wanted to give Ash a Mega Evo, but couldn't since no Gen 6 Pokemon except Diancie have Megas, so they had to make up a new form for Greninja instead. Besides, 10,000,000 Volt Thunderbolt is basically Pikachu's equivalent to the Bond Phenomenon.