*IF* and *WHEN* they introduce custom chocobo I'd like to see, it done through a system similar to the character creation system.

Allow you to choose different styles like Anonymoose suggested. But maybe each style has it's own attribute .
for example. You can choose different beak styles.
Style 1is great for digging or sensing burried treasure
Style 2 is more pointy and is better for combat roles
Style 3 is more thick and broad, it adds a lot of defense.
Body:
style 1 is lean and slender allowing it to run long distances
style 2 is more bulky, its good for cargo transport
style 3 is muscular and is great for combat.

ect ect.

In my minds eye I envision a system where you raise a custom chocobo from egg to adult. You can then register your adult bird at the local Chocobo husbandry club. There you can breed your chocobo with other registered players to create a new generation of chocobos.
You can can look at the different "stats" or colors and pick and choose with what bird to breed with.

As long as the system is deep and complex to keep players interested but user friendly and approachable as not to deter players from delving into custom chocobos.