I think it'll be cool but I think she doesn't need it if the only choice we have is to face her in double battle since her team is already challenging enough for double battle most of her pokemon have a good synergy also it's not too hard to take out. Adding mega charizard to mix will take it too far in my opinion.
However If player have a choice to fight her in single or double battle with different team like Amaria, I think mega charizard Y will be a good boss pokemon in single format for player to get over also talk about how epic it is.