I've never read that fic where his control was such an issue. I've always had the opposite problem. Naruto's control issues get hand-waved. "I can't make a bunshin because I simply have too much chakra to do it, but here's a list of four hundred elemental techniques I can do with zero effort." I would never make his chakra control worse than I perceive it to be in canon.
As far as "the basics" being the issue, as far as I'm concerned, that's really just generalizing the problem. I specifically singled out chakra control because not *ALL* the basics are a problem for Naruto. His taijutsu is adequate and while his infiltration skills are not even close to what fanon gives him, he did manage to get the jump on Sasuke and tie him up in like chapter 2 or 3, so again, quite adequate.
If you're arguing that "the theory" is his weak point, well I couldn't disagree with that I guess. Naruto even calls himself stupid when he meets the Fourth.
Those pics. Love it.
Story. I think the big questions right now are ones I don't entirely want to answer. I'm comfortable with the general background and assuming I actually write this I will start by working some glimpses of Minato/Kushina/Konoha before the Kyuubi attack. I've already decided to disregard the standard novel format in the beginning. The most interesting way to invest readers in this comes back to "show, don't tell" and if I just "tell" the back story in a prologue it will be boring. But if I start from the time of Minato being a gennin and chronicle his life up to Kyuubi that will be far, far too much of a commitment from me in terms of time and energy.
When I say the big questions I mean: What will be Naruto's first "real" mission? How exactly does the war break out? What will the final battle look like and what kind of build do I need to get there? Will Naruto have a love interest? If so, who? (I've already labeled Samui as a possibility, but that's still just a possibility.)
The reason I don't entirely want to answer these questions is because I don't want my writing to go in a different direction than my goal. A long time ago I was working on a story called "Path of Hatred" that had that happen. Naruto was supposed to go one way when he seemed to be going another. I found myself written into a corner.
I guess the only other thing is wondering about just how much AU I want to pull in. In many ways I want to keep this as a believable divergence to the canon (diverging at the Kyuubi attack), but especially given what just happened last chapter they may be stuff I need to throw away.
An increasing concern is the way the bijuu and the history have developed. Just as an example, when I first picked up this manga, I had the belief that the Fourth was this super baller who sealed away an unbeatable monster, and that this put him on a pedestal as great even compared to the other Hokages. But the way canon has developed, there's a part of me that can't help but wonder if he was actually the weakest Hokage (at least before Tsunade). The First could control bijuu in raw form and create entire forests from nothing. The Second we don't know too much about, but it was said that he also mastered spacetime techniques. The Third was the God of Shinobi who in his prime could face down all three Sannin and defeated both the First and Second at least in their Edo Tensei forms. And this at a very old age.
I definitely want to write the Fourth as a baller. I want to write him as the kind of guy who, if the current manga chapter happened, would break free of Orochimaru's control and tell Sasuke "touch my son and you're fucking dead." Unfortunately, given how much Kishimoto loves Sasuke, the most likely situation is that Sasuke could face all Four Hokages and win. After all, we know that Sasuke is going to fight Naruto at some point and we know that with how powerful Naruto is, Kishimoto will feel the need to remind us that Sasuke is "on a higher level."
Sigh. Maybe I'm just too bitter about Post-TS.
