The biggest problem in your story is the lack of povs (points of view).
There are no reactions to his feats, there are no feelings what so ever.
In the entire story, there is just one time we saw some reactions, when Hiruzen talked to Danzo about him, there were a lot of chances for you do it, when he was with Mei Terum you should have shown it from Mei point of view and Mei and Hiruzen reactions after he left, naruto reaction when he becomes a missing-nin, and a lot more (pov) especially Shikamaru's, his analyze are always cool, or anyone opinions on the matter, his team members, even some citizens will do, etc...
And something else bothers me, why does everyone think he is a citizen? you didn't mention any records of him, no father or mother, nothing, maybe he was an Uchiha that slipped away somehow, he can close his Sharingan after all which was shown to be impossible without being an uchiha, and I fail to see the village just leaves orphan kids to fend for themself. and living in a secret place is much more suspicious than him getting some money...