I feel like Pain would have been a stronger conclusion, but the war arc touched on a lot of supernatural themes that the series had been carrying since the beginning.
It's all well and good to have a ninja world, but things like the Nine Tails felt out of place from the start. The tailed beasts were always important to the story, and investigating their origin during the War arc and beyond added a level of closure to the story that ending with Pain couldn't have done. That said, keeping the beasts as a mystery would have been an alright ending, too, but what we got wasn't as left field as people usually claim it is and actually built off the rest of the series' scaffolding in a lot of ways. Things we got from going beyond Pain:
-Seeing more of the other villages/parts of the ninja world
-Seeing the five kage
-Closure to Danzo's story/Root subplot
-Sasuke finally escaping the "kill Itachi" shadow he'd been living under for the entire series
-Madara and Hashirama's backstory and the history of the hidden villages
-Learning what was on the Uchiha tablet (HUGE hints towards this throughout the series)
-Learning why the tailed beasts exist
-Tobi's identity
The only things that were really out of place were Tobi = Obito (although this was pulled off decently, I would have preferred Tobi actually be Madara or someone entirely new) and Kaguya's revival. Sage Madara was enough a final villain for Kaguya to feel entirely unnecessary, although you could argue that she needed closure as the series' real big bad ever since we learned her role in creating the ten tails. I feel like the techniques being used had to reach astronomically high levels of power because we had finally gotten to the be-all, end-all of a series that had insanely powerful creatures (Nine Tails) from the beginning, and they had to contend with that somehow.
Naruto and Sasuke ending things basically by themselves and the insanely rushed nature of the last few battles show how this all occured by Kishimoto writing himself into a corner, however. The last few arcs lacked a sense of refinement and things like Zetsu and his real identity, and the villain changing every fifty chapters, felt really wonky. I think it's possible to defend the decision to continue the series to the point that it got to, conceptually, but it's undeniably full of flaws in its writing and I can understand why so many people take issue with it.