So, we get this since everyone's fucking torn between thirty bazillion things;
>Deoxys and Mewtwo play important side-roles in the game
>Deoxys can be found at a research facility in Pokemon X, while Mewtwo can be found in a cave in Pokemon Y
>Deoxys runs from you four times, showing off one forme each time, and then staying in the forme that matches the highest stat of your first pokemon. SpAtk/SpDef count as Atk/Def, respectively
>The head scientist explains how Deoxys is a quick thinker, rushing through and learning on the fly.
>Mewtwo does something similar, in that you fight his original forme in a cave match. He blocks the pokeball every time though
>Defeat him, and he heals to full in his new forme. He can be captured then
>A spelunker/researcher explains how Mewtwo is calculating and reserved on judgement, rather than acting rashly.
>Champion will be up a tower with twin spiral staircases
>Choosing the blue side, dubbed the X stairs, prompts the champion to say how you prefer to think before acting.
>Choosing the red side, dubbed Y stairs, prompts the champion to comment on how you live for the moment, and deal with situations as they arise
Or something like that. Not a perfect theme, but I'd hope the idea is understandable.