IMO, there are some definite differences between the 2 Poké and these differences provide some distinct advantages you can leverage given the particular deck you are running. For example, consider that both Poké have/can:
- Good support like Fiery Torch and Blacksmith that could also be leveraged.
- CC Retreat Cost.
- 180 HP.
- 2 attacks.
- Take advantage of DCE in order to accelerate required energy attachment.
From this list above, neither Poké has any distinct advantage; nothing yet distinguishes one as being "better" till you closely examine and compare their respective attacks.
Charizard XY 11 has Stoke and Fire Blast attacks for C and RCCC energy cost, respectively. Stoke does not inflict damage, but provides the opportunity for you to search, get and attach up to 3 Basic energy cards to this particular 'Zard depending upon a favorable coin flip which has a 50-50 chance of being successful. Fire Blast only inflicts a sub-par 120 damage for the energy cost and one must also discard an attached energy.
Charizard XY 12 has Wing Attack and Combustion Blast attacks for CCC and RRCC energy cost, respectively. This 'Zard's first attack inflicts only 60 damage, but since it is a Colorless energy attack, it becomes very versatile and can be teched into a variety of decks (e.g., Seismitoad EX that runs only W energy) that do not run R energy. Combustion Blast inflicts a solid 150 damage for the energy cost and with an attached Muscle Band can 1HKO many big HP Poké in the format. But, that Poké can't use Combustion Blast during the player's next turn. The great news, however, is that you can attack multiple, consecutive times with this 'Zard just by getting it back to your bench (via Switch, Rush In, etc.) and switch it back to the Active position.
I only run the Wing Attack/Combustion Blast Charizard EX in my decks; for I see no advantage/reason in running the other 'Zard.