I disagree, that is precisely why it would do harm, because none of Ash's current roster could hope to reach to Charizard Y's potential, even a potential Mega Greninja would look like a complete joke in comparison.
The only way I can accept this happening is if we get the same case as AG, with Charizard appearing in specific high-level battles, while other lesser battles are given to proper Pokémon*. OR, if we get a Elite Four arc.
*In which case, Charizard would not be the sixth member. That title would belong to someone else, whoever that might be.