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Laptop PC. I find it kind of weird that it'd be left behind on such a journey.
Ability to buy more boxes with the shitton of money the games throw at you. Small number to keep Bank relevant. Maybe an option to switch out a Pokemon's ball for a fee + some arbitrary "bonding time" in the Center.
Anime egg patterns.
Grass immune to Fairy / Fairy Absorb ability.
More Region-based form differences.
Custom ball-throwing animations based on overall "style" (Lumiose level, clothing, type, etc). Same applies to picture poses.
Friends and rivals call you up for random battles in random picturesque places with scaling difficulty.
More interaction with your mother. Seeing her on TV interviews after you become champion, sending you items, whatever.