vexen should have a ditto or at least a dark or ghost type because he has anti sora, a copy of sora, the rest of it is pretty good though!

Zexion NEEDS a Zoroark. They are Illusion masters

I like most of your choice, however your choice is not very match. You can gave (Legendary):
Xemnas: Arceus, Regigigas, Mewtwo,
Xigbar: Palkia, Deoxys
Xaldin: Lugia, Rayquaza, Tornadus
Vexen: Articuno, Regice, Kyurem
Lexaeus: Groudon, Terrakion, Regirock, Landorus
Zexion: Darkrai, Giratina, Zoroark
Saix: Cresselia
Axel: Heatran, Ho-oh, Moltres, Entei, Reshiram
Demyx: Suicune, Phione, Manaphy, Kyogre, Keldeo
Luxord: Dialga, Cobalion, Genesect (, Celebi)
Marluxia: Shaymin, Celebi, Virizion
Larxene: Zapdos, Raikou, Zekrom, Thundurus (, Mesprit)
Roxas: Latios, Jirachi, Mew, Victini (, Azelf, Meloetta)
Xion: Latias, Uxie (, Mewtwo, Meloetta)

I had to admit, I really confuse about Xion legendary. But I think she deserve Latias and Uxie. I don't know about Mewtwo and Meloetta. But if Xion had Mewtwo, then it will be perfect Mew for Roxas and Meloetta is Psychic and Fighting type, made Meloetta suitable for Roxas.

What about Xion? Okay, so she may not REALLY be a part of the organization... But still. Maybe you can add Phione, because it is the child of Manaphy who has power over hearts. Need I explain further? And perhaps Mewtwo or something or Ditto because she is fake. Girafirig, because giraffe's cannot talk because their lungs are messed up and it has a dark side, like Xion at the start. And, I dunno, Unown, because she is forgotten at the end like how Unown is not understood.

Whoa. This is awesome. Good work assigning the Pokemon!

Nice.

Most of this was very accurate and entertained me a lot.

I especially liked how you gave Marluxia and Demyx the darker side that no-one else seems to do.

This was super cool! I found this on someones' favorite stories list and I find it interesting how I knew nothing about Kingdom Hearts, but now, thanks to you, I have a grasp on the characters with your shrewd usage of certain Pokemon to describe their personalities. That is the mark of a good writer I think, you can take a subject that someone may not know anything about, but enable us to get a grasp on it in one story!

..woah..this is pretty..insightful..

Really interesting way to match-up the Organization with its own Pokemon. Though, I'll bet Larxene won't take kindly to be considered a parasol lady, hehe..