There aren't any loose ends to tie up unless you want answers to every tiny question in the series. And that doesn't warrant a Part 3.
We still don't know how to movie ends, so there's no way to say there will be a Part 3.
Who really is Kaguya Ootsusuki?
Who really is Black Zetsu?
What happened between the previous transmigrants of Indra and Ashura?
How did Indra and Ashura's fight ended, was it a tie or either one of the brothers die?
Why is it that there is no mention of Hamura in history records?
Was Uzumaki clan descendents of Hagoromo or Hamura?
How did the Ootsusuki brothers initially received the Sun and the Moon seals?
What happens to the Bijuu?
How did the Uzumaki clan receive their specialty in sealing?
Who are Tsunade's parents?
How were Jiraiya's travels?
Why is it that the Uzumaki ceremonial masks share a close tie with the Death Demon?
Are there other beings like the Death Demon
Who are Naruto's grandparents?
When did Itachi's sickness began showing itself?
Did Izuna really gave his eyes to Madara or Madara steal them?
What kind of character was Izuna, compared to Madara?
What were the doujutsu(Koto Amatsukami, Kamui, Amaterasu, Kagetsuchi etc.) of Izuna and Madara?
Madara referred to Tengen Shinsei as being an Uzumaki jutsu, was there reasons other than the sealing prowess that the villages feared the Uzumaki?
Is there a connection between chakra chains of the Uzumaki Clan and that of the Gedou Mazo?
Are the chakra chains a Uzumaki Kekkei Genkai or limited to females of the clan?
Is the chakra adaptation a Uzumaki Kekkei Genkai or was it only special to Hagoromo and Naruto?
How did Hagoromo preached Ninshuu?
For all the time that Madara was alive, did he setup any other plots?
Were Hagoromo and Hamura twins?
What is the relation between Rinnegan and Byakugan; and why is that Hagoromo had the Rinnegan and Hamura had the Byakugan while their mother had the Sharinnegan and Byakugan?
How did Madara got infected with the Black Zetsu?
Was the Uchiha tablet modified and to what degree was it modified?
Was the rabbit-headed being that spat out Madara was a Bijuu or Kaguya or the representation of Gedou Mazou's shell?
Who was the father of Hagoromo and Hamura?
With such great healing prowess, did Hashirama really die from his battle wounds, got killed (if killed by whom) or died of old age?
If Hashirama died of old age, why did he entrust the village to Tobirama while still being alive?
Who was strong enough to kill Tobirama?
What will now happen to Kabuto?
What will happen with Orochimaru?
How is Juugo's clan prevalent in sage-chakra usage?
How did Madara dictate the Eight-Gate Release when taunting Gai although he had his ass handed to him as the Jinchuuriki of the Juubi?
...and I could list many many more down the line.
