You must have read it wrong.
"All of the characters to consider were on our internal roster from the beginning of development. We had a slot for a new Pokemon reserved, but did not wait for X and Y."
Which says they wanted a new Pokemon, they didn't know which one at the time, but clearly had no idea what they wanted. They said they had a slot for
A new Pokemon, not specifically one from X and Y. They didn't want to wait for X and Y to release to see what was popular, looked at early reference drawings (i.e., concept art) and picked Greninja.
If there was ever a placeholder, it probably said 'New Pokemon' or 'We want a new Pokemon representative' or something along those lines, and not 'Pokemon from X and Y'. The fact that X/Y was developed right next to Smash, essentially, was a happy coincidence.
Like I've said already, all this really says is that the guy only has access to E3-related promotional material.