>>21424123A mary sue is a character that serves as an idealized figure that can do no wrong, is always portrayed as being superior to others and often serves as an avatar of the author. Which of these things could possibly describe Greninja? It's not really portrayed as having any personality, there's nothing in the game pointing to it actually being superior to the other starters, it doesn't have any ideals to speak of and it's almost certainly not an avatar of any of the authors of pokemon.
What you're saying is literally like saying "this choice between pizza or hot wings is really a catch 22" when you're trying to decide what to have for dinner. That's not what that phrase means and using it in that context doesn't make sense.