Currently writing a Naruto Crossover right here, so check it out if you want. (You know you want to) Yet while I was thinking on it, I had other ideas put down in the Naruto forums, and I figured, maybe someone over here would like to look at them, so I posted the first story idea I wrote over there. I'd honestly be willing to work as editor for you if you wanted to write the story, so if you want a story idea, an editor and a Naruto/Crossover idea/story list I'm your dude.

Idea #1:
Naruto in Equestria right? But in this one he's been reincarnated as a changling with his blond hair, normal or end of series(EOS) one, his eyes are not unlike Chrysalis's in that he has actual working pupils and irises. How big he is? Above average, so say about the size of Twilight post-Alicornization. He's a changling with a horn, and no wings. You can change his color if you want, I don't mind, though I'd either make him orange or the normal black.

Premise(Not too well thought out but this is what I came up with): He was a baby changling that got separated in Everfree back when Chrysalis started getting power-hungry. From there he would survive for say 3 years before being found by Zecora and unofficially becoming her son. Now due to being her son, he has picked up on he lingual quirk, but he only speaks it to her and her alone, at least until he's close to someone. You can play this off, as a way of knowing if he likes someone more than a friend, with Zecora familial(Motherly) love, and someone else outside his family obvious. So he's been with Zecora for say 15 years after being found and he is well versed in her arts of potion making, gardening, etc. Not only this but he makes a habit of challenging the creatures of Everfree, so he works his way up the ladder from timberwolf, wolf pack, snakes, cockatrice, manticores, the two dragons in the forest/ursa minor, and whatever's left. He's just strong enough to injure a manticore but he can't beat one by the show start.

First Encounter: Now I had two ideas for this one. Either we can have him have been interacting with Ponyville from the moment he knew how to transform, so say he made up a personal appearance that mixes between Zebra and Pony, to be unique ya know? Also he's actually well integrated into the village, his disguise not his true form, so he's not unfamiliar. Mostly to AJ's family due to always buying some apples from them. Now for the encounter idea, he's learning how to touch into the World Well, which is basically Nature Energy or Cosmic energy if you want, and as he's meditating on top of the water he get's happened upon by Fluttershy, sort of. She sees something in the forest(Naruto(true form) training) and he doesn't notice. So here's how this one can work out.

There are two paths to go from here: Now the encounter can change due to WHEN we introduce him.

It will either be show beginning or sometime after the changling invasion on Canterlot.

Another thing is Naruto has no inkling of what happened in Canterlot, due to the fact that he was traveling somewhere in Saddle Arabia looking for a special Herb for Zecora. So when he gets back he's more or less unaware of the status quo changing for changlings, so yea blind man walking into street sign bad.

So back to Encounter idea, Fluttershy gains the attention of Twilight and they go into the forest. Now remember that this could be after the invasion so Twilight's opinion on Changlings is....Not so optimistic, to put it lightly, or if at show start she could be just fearful due to rumors. So the encounter happens, and we have (A: Show start) situation where Twilight tries to speak with Naruto, or (B: After IoC) Twilight takes it upon herself to rid them of the changling, due to past tempers ya know. Now Naruto's response to this is (A: Run away into the forest hiding from them via illusion magic) or (B: Fighting back, or pranking the everloving hell outta Twilight).