So far kishi has been a great writer(in my opinion). Whether he turns out to be just a good writer, I wont know until the end of the series.
However here are the flaws that stop kishi from being an incredible writer.
* Lack of developing side characters a bit more(This story is a story focused around Naruto. I get it. But you could just give us a arc, in which the side characters(such as k11) get a bit more development. )
* Due to the above, not takeing full usage of the war arc(edos). He couldve given each of the k11, a fight which their abilities are really tested. Where they get good development. He couldve had a sasuke pursuit arc(fighting sound 4) type fighting(though not people fighting to let others ahead, but fighting to defeat).
He couldve really had a few more fearsome edos(or at least given them more paneltime.) He couldve shown that while the leaf village is very strong, that other villages are not like fodder(or only have like 3 strong people). He couldve expanded the world a little bit.
* He somewhat wasted reviving the edo hokages. He currently just let them get fodderized by madara(which Im fairly sure has to do with just showing just how strong he is), but he couldve at least let them land a blow or 2.(then get fodderized)
He couldve let minato do his long named jutsu, and it turns out to not have affected juubito, or that obito used a clone jutsu or something.
He just couldve shown a bit more. I understand he ultimately needs them to be defeated because the juubi jin, is just that much more powerful, and that he needs to follow his theme of "the new generation surpasses the old", and "the old generation entrusts the future to the new", but he still couldve given more fight scenes.
* He couldve shown us why a character is justified/earned their nickname. Kakashi learned 1000 jutsus. Let him show 20 or so in succesion. Guy is the wild green?(blue?) beast of konoha. Let him go beast a little bit. Minato is the yellow flash? Run on sight? Let him show us more of why he earned that reputation.Hiruzen is the professor, and knows "all the jutsu of konoha"(i dont think so....i doubt he can use hyuuga techniques etc), let him show jutsus from different clans. Hashirama had legendary healing? let him show that healing. etc etc. He hasnt just ignored it, but he hasnt expanded on something he couldve done, to make the manga more rich.
*He didnt devolop enough characters from other countries, to make them feel even close to konoha level. Right now it feels almost like konoha is able to take 3 countries or more at once(though they cant)
*Obitos diologue couldve been much better. The whole Im really good, then im corrupted then im redeemed thing, works fine. But the diologue couldve been better. Not mentioning rin every 4th sentence wouldve been better.
Most of my complaints, are just missed opportunities kishi couldve taken.
I dont really have many issues with what he does in the manga. Its more of what he doesnt.
Naruto will probably remain my favorite manga. But it probably wont go down in my books as a masterpiece.(ex. Avatar the last airbender. It was interesting, had good plot movement, and pace, no major plotholes, is rich with characters, and has a good beginning and ending, and characters feel natural, and develop properly.)
Onepiece, is a manga i can see being a masterpiece. It will probably still have the plot no jutsu, and plot hole no jutsu, that goes on, but it doesnt affect the storyline or theme. The plot progression and character development, and richness, make it seem like it will become one.
Kishi has made a great manga. Sure its probably not gonna be incredible(he could still turn it around, and make a REALLY good ending), but it will be pretty good.