Square DID made a RPG game with Nintendo for SNES, the game is Super Mario RPG.

For this game (It will not be a joke!) I can put a list of what/how Nintendo can add to Kingdom Hearts:
1) Add Nintendo based worlds
2) More ally characters
A) Link
B) Samus
C) Mario
[There may be more of them]
3) More summon characters (mostly Pokémon)
4) More equipment (Weapons, Armor, Accessories, Items)
5) More kind of abilities (Limits as well)
6) More Nobodies
7) More Heartless (But not too much)
8) More other enemies (That doesn't fit in Heartless or Nobodies)
9) More Bosses
10) More Gummi Ship (the minigame)
A) More Gummi Routes (Based on how many new worlds has been added)
B) More Gummi Enemies
i) Normal (White/Blue)
ii) Normal (Red)
iii) Normal (Yellow)
iv) Rare (Boss like)
C) More Gummi Ship Models
i) Main Ships
ii) Teeny Ships
iii) Ally Ship/s (eg Samus' Ship)
D) More Abilities
E) More Material Gummies
F) More Deco-Gummies
i) Projectile Gummies (Weapon Gummies)
ii) Lock-On Gummies (Weapon Gummies)
iii) Slash Gummies (Weapon Gummies)
iv) Inpact Gummies (Weapon Gummies)
v) Engine Gummies (Movement Gummies)
vi) Wing Gummies (Movement Gummies)
vii) Cockpit Gummies (Auxiliary Gummies)
viii) Sheild Gummies (Auxiliary Gummies)
ix) Optional Gummies (Auxiliary Gummies)
G) More Paint
H) More Upgrade Levels:
i) Main Teeny Number Limit Upgrades (New)
ii) Main Cost Limit Upgrades
iii) Main AP Limit Upgrades
iv) Main Teeny Cost Limit Upgrades
v) Ally Cost Limit Upgrades (New)
vi) Ally AP Limit Upgrades (New)
vii) Ally Number Limit Upgrades (New)
viii) Ally Teeny System/s (New) [On one ally each]
xi) Ally Teeny Cost Limit Upgrades (New)
x) Ally Teeny Number Limit Upgrades (New)
xi) Main Teeny AP Upgrades (New)
xii) Ally Teeny AP Upgrades (New)

This is far as I got.