I would go with something more along (Battle) Illusion Clones Jutsu. I even got a backstory for the technique.
To summon a clone, you must know enough about the person you are about to summon, ex. at the beggining of the game you know enough about Naruto, because you have been buddies for a long time, so you can summon his Illusion Clone.
If you want to summon ex. Kabuto, you need to go on lots of missions (survival trial) and repetetively face him, so you can learn more and more.
Knowledge in this game is refered to as fragments, which would also make sense with getting them from Elite Instances. I mean, you are facing the person you collect data about, so battling them is a great way to do so.
Star upgrading also fits well, since the more you know about the person, the stronger your clones become.
You have control over action of your clones, while they still regain the intelligence of their oryginal, which would explain Standard Attacks and Passives even working. (You can't just "cancel" passives, or standard attacks). Mystery Abilities is the only part that is under your control, which also works in combat.
ANBU just sent us on this mission so they can watch how our character develops his ability in this technique, and tries to encourage him to get stronger in order to protect the village.
Clone jutsu that almost all mains have (I think that Earth do not, but I'm not sure) is a proof of how little we know about ourselves, since they usually die very quickly, and are not very profficient in combat (in most cases).
Main character is along the lines of the villages Secret Weapon, like once it was with Jinchuriki, but this time around, only Konoha has it. It is kept a secret, and during next War between villages, we are going to be sent to the battlefield, to make our enemies face their friends, families, and even themselves! XD
I got too deep with that, but well, it's just a theory :)