For all the details put into the world of Naruto and Naruto: Shippuden, there seem to be a lot of loose ends mangaka Masashi Kishimoto either never got the time, opportunity, or budget to flesh out properly. Hope was granted when Boruto: Naruto Next Generations was greenlit, though it could only do so much.
This series produces quite a few answers to questions fans who grew up with the show probably asked themselves, including those who decided to write fan fiction on the topic when they weren't satisfied. But there are still many mysteries left unanswered by the original series and its sequel.
10 How Does The Hidden Leaf Deal With Orochimaru The Traitor?
Orochimaru is no stranger to the Hidden Leaf Village but was not quite ousted entirely by the events of Boruto: Naruto Next Generations. Although he did lead a plan with the Hidden Sand to destroy Konoha, he ended up helping the Allied Shinobi Forces during the 4th Great Shinobi War to defeat Madara & Obito's Eye Of The Moon plan.
We know by this point that Mitsuki is an experimental child of Orochimaru that is allowed to be in Konoha, but what of the man himself? Where does he reside? Tsunade understandably continues to hold a grudge against him, but what about the rest of Konoha?
9 Could Sasuke & Naruto Defeat Madara?
It could be said that because Team 7 could defeat Kaguya, the one who removed Madara from existence during the final act of the 4th Great Shinobi War, it should then be possible for them to have defeated Madara, right?
But take into account that the move used by Naruto to capitalize on the opening Sasuke created using Amaterasu on Kaguya might never have worked on Madara (unless he was into that), we have to wonder: Could Team 7 have finished out the battle & defeated Madara? Would Konoha's #1 Most Unpredictable Ninja have found a new angle to exploit instead?
8 What Does Hinata Really Want To Do?
It's no secret that Hinata Hyuga's clan did not think very highly of her abilities as a shinobi for quite some time. Even though she had the bravery to confront Pain in his battle with Naruto, to at least buy Naruto some time, she did not have the skills to hold her own against him. From the events of The Last: Naruto The Movie, she appears to have lost the ability to maintain a grip on vertical surfaces by concentrating chakra on the soles of her feet.
So, what now? Is she content to play housewife with her accomplished Hokage husband, Naruto? Or has she continued to train with her clan in order to protect the village, should another invasion of the Leaf arise?
7 How Was Kakashi Able To Use Susanoo?
Kishimoto, what were you thinking when you gifted the abilities of the all-powerful Sharingan to Kakashi after Obito had passed away?
Did Obito gift him the rest of his chakra in his dying moments somehow? Did Kakashi master the use of the Sharingan just enough for one final impressive feat to end the fight with Madara? Were you backed into a corner, unable to find another way for Kakashi to be useful during this war for the fate of the ninja world?
6 Where Do God Trees Come From?
Chakra is a strange thing in the Naruto universe. It is related to your bloodline, following all the way back to Kaguya Ōtsutsuki's arrival on Earth. If you follow it back farther than that, the Ōtsutsuki seem to travel planet to planet seeking the chakra fruit of the God Tree in order to maintain their powers and theoretical immortality. But where did the seed of this tree come from?
Was it sent into space by an even bigger God Tree? Or sent out by the Ōtsutsuki themselves to be harvested, once it had consumed enough blood to bear its Chakra Fruit that sprout once in a millennium? This question remains unanswered, but given the involvement of the Ōtsutsuki in the events of Boruto: Naruto Next Generations, we may eventually learn the answer.
5 What Would Madara Have Done After Controlling The World With The Infinite Tsukuyomi?
For having quite a lot of time to think over this plan, there seems to be one major oversight to the Infinite Tsukuyomi idea: no one trapped inside the genjutsu could ever reproduce. Those trapped in the gaze of the Eye Of The Moon plan are left theoretically unable to move or interact with the world outside of their own minds.
In practice, they are actively leeched of their life force by the God Tree until they become mindless White Zetsu. Did Madara plan to let the entirety of chakra control-capable shinobi die out, as a path to "true peace?"
4 Who Is Rock Lee's Significant Other?
Rock Lee is a bit of an enigmatic figure himself. His efforts through Naruto and Naruto: Shippuden to "woo" Sakura may have been a bust. However, from Metal Lee's existence in Boruto: Naruto Next Generations, his efforts clearly weren't entirely for naught. There may or may not be a Lee clan in Naruto, but Rock Lee seems to have been hard at work expanding his bloodline.
So the question is... with whom? It could be Tenten since they had much time to bond being on the same ninja team together especially after Neji's death in the war, though this is never clarified.
3 Who Are Rock Lee's Parents?
There hasn't been much information disclosed about the Lee clan, considering that the only member featured heavily is Rock Lee. He was taken in by his mentor and lookalike, Might Guy (commonly referred to as Guy Sensei).
Given that they dress identical and even have the same bowl-cut, one might assume that Guy is his real father, but they aren't blood-related. Rather, Guy is just Rock's irreplaceable father figure. There's almost no information given about the Lee clan, so it's surely impossible to discern this answer. Who are his parents?
2 Where Are The Other Planets The Ōtsutsuki Have Visited?
The Ōtsutsuki is an enigmatic alien clan with immense powers and a deep involvement within the Naruto universe ages prior to Naruto's birth. The story goes that Kaguya Ōtsutsuki arrived on earth a millennium ago with a few members of her clan to search for the chakra fruit from the God Tree in order for them to maintain their power levels and quasi-immortal forms.
This leaves a few questions: Where did they come from? How far away is their planet? Do they hail from a different dimension? How many of them are there, and how long has their clan existed? These are questions that the Boruto-verse are more likely to answer than many others, considering that the Ōtsutsuki clan has a huge role in the anime. Expect to see more details about them, the God Tree, and possibly a glimpse into their homeworld.
1 Are There More Uzumaki Clan Members?
This is a question thought to have been answered already but by the time the Pain's Assault arc of Naruto: Shippuden ends, there have been two false positives already. Both Karin of Sasuke's ninja groups, & Nagato, the "leader" of the Akatsuki, at different points were revealed to be members or descendants of this once-powerful clan! Tragically, this village that once populated the now-defunct Uzushiogakure (The Village Hidden by Whirling Tides) mostly met their end when an undisclosed alliance of various ninja from different villages decided to eliminate the clan.
They were afraid of their incredible life forces & mastery of fūinjutsu (or Sealing Techniques). There was never proof that the entire clan was slaughtered, given both Naruto and his mother's existence, as well as Karin and Nagato. So there is a possibility that out there somewhere, a distant (or not so distant) relative of Naruto could still be alive!