But most of those were for movies, non-canon plot purposes, and the meteor in Rayquaza's body acts as it's mega stone not to mention it did it when it was near that gigantic keystone thing.
I mentioned this theory a lot of times. If the player exceeds the maximum amount of turns it's in battle, both pokemon and trainer will white out, making it an instant loss. That's how I imagine it would work.
Like you say those Pokemon's forms were for movie purposes and non-plot purposes, there's not rule stating Zygarde's forms and Ash-Greninja can't be treated in the same manner, as something purely to move along plot and the anime. If the anime were such an advertisement, then every little aspect of the anime would be included in the games, yet they weren't. The Tripokalon is still a strong example of this; it was a major plot point for Serena (the character, mind you, based on the in-game counterpart), and we never saw it in the games. It can exist in the anime without existing in the main series games. Side-games can allow this, and as someone pointed out, those forms help boost sales of those side games.
You could always just save it for last, or not use it at all. There are options. Also, do people keep getting the idea that customization won't happen because of this? How hard do they think this is?
Yes, there are options to this, but as mentioned, hardly a handful of people will want to even BOTHER with that Pokemon mechanic if it means an instant loss in some way. I know I personally would never touch it if that were the case.
Customization being included in the games, especially to the extent of XY or even further, would cause the developers to have to model and color more than a dozen forms for each of the Pokemon given this "synchro" mechanic.
EXAMPLE: Greninja.
You are a male player. The mechanic uses hair color and shirt/top color. The male character is given four hair colors, plus over 1 dozen shirt colors/patterns. This means almost 50 combinations of colors/patterns used on Greninja alone to "synchro" with the character's customized look. Imagine getting more customization options (in this case, two more hair colors and 4 more shirt patterns/colors), that takes you to almost 100 combinations for ONE POKEMON ALONE. And that's keeping it simple on just hair color and shirt color (as you pointed out would be the choice "traits" that Pokemon would get.
That is not logical at all. Not for the developers. Imagine the three starters from Kalos getting it, plus the ones from this new gen, plus a handful of other gens and so on. How many thousand combinations will they have to make? How many thousnads of different models will they have to spend months making JUST for one mechanic of the game that many won't use because, as you suggest, it will cause instant losses?
Mega Evolution as being the special form of Ash-Greninja is sounding more and more like a valid idea, and one that makes sense based on Rayquaza alone. Max-friendship being the key to this form of Mega Evolution could make it stand out. Or just giving them mega stones because in the anime, all kinds of evolution rules are broken, so this could be one of those cases.
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