I feel like this must have been recommended before, but if so I couldn't find where, and it has just recently been updated after a longish pause. I just recently read through what there is so far of Lighting Up the Dark. I wasn't familiar with Naruto, but I was generally able to follow it, and I liked some of the humor (which seemed to be poking fun at anime generally, rather than being specific to Naruto). It was inspired by an omake chapter in HPMOR (which is why I thought it would have been mentioned around here at some point), and presents a fairly interesting, rationality-upgraded Naruto.