When it comes to villains in Naruto, there are five that stand out among the rest. Orochimaru carried the first half of the series as the antagonist and Itachi is one of the best crafted tragic villains in recent memory. They were more antagonistic towards Sasuke, however, and the third villain, Madara, was more of a villain to the whole series.
That leaves Pain and Obito as the two who could stand up as Naruto's greatest foil. Both of them had a direct impact on Naruto's life, from Obito pulling so many strings in the past and Pain the one who killed his mentor. The question is, which one is more fit to hold the title as the greatest foil.
10 Pain: Destruction of Konoha
The destruction of Konoha will always be the peak of Naruto in the eyes of many (until the end of it). It showed that there would be real ramifications for picking fights with Akatsuki and showed just how powerful they were as an organization when their leader could single-handily take on an entire village by himself. The battles there were also excellent, from Kakashi trying and failing to stop him, to Naruto's epic arrival on the scene. It's still one of the better fights in the whole series.
9 Obito: Connection To Kakashi
While Jiraiya certainly had a huge impact on Naruto's life, Kakashi is always going to be his first true master. Their bond is huge and a big part of Naruto's character. By proxy, the ties Obito has to Kakashi's past affect Naruto himself. Their relationship in a way mirrored Naruto's rivalry with Sasuke, making him look at his own life through a different lens. It's part of what made making Obito the man behind the mask such a smart call.
8 Pain: Killing Jiraiya
This is the big one in Pain's favor, the one action that made him an instant enemy of Naruto. Jiraiya had one of the biggest impacts on Naruto's life, personality being as jovial and happy as Naruto's was when he was younger.
Having a father figure like that die is heartbreaking, especially when they were never even able to retrieve his body. The battle itself is one of the most emotional in the whole series as well, one of the greatest ways to introduce an adversary like Pain.
7 Obito: Starting The War
Starting a war so large that it required the villages to unite as one is nothing to scoff at, a feat that not even Pain can come towards. In his way, Obito had already achieved a level of peace before he even tried to enact Madara's moon eye plan. He succeeded in getting the villages to put their differences aside to stop him, making him a martyr. That wasn't enough for him, however, pushing it to a level that forced action to be taken. The number of deaths he had a hand in is massive.
6 Pain: His Past
Pain's past and how it shows that Konoha wasn't always this upstanding village that sided for good was great. The way it showed what an utterly despicable human being Danzo was helped make his end at Sasuke's hands feel so good. His past was very relatable as well, showing that he was a victim of tough times and wasn't able to overcome them in the same way that Naruto did. He's an example of what Naruto could have been, had he let the villagers disdain for him turn his view of the world.
5 Obito: His Turn To The Side Of Good
Obito's turn to the side of the good, while telegraphed from a mile away, was done better than Nagato's. They both felt like they were doing things for the greater good, trying to bring about the same thing, more or less.
The difference is that Obito was doing it all for one person, Rin. Nagato, meanwhile, was harboring so much ill will for what happened to his friends and his village during the wars. Obito also had a direct connection to Kakashi while Nagato didn't, making the talk no jutsu feel more effective.
4 Pain: Abilities
For as cool as the final fights were during the war, even Madara's skills paled in comparison to what Pain brought to the table. His abilities were so far above everyone else when he got introduced that he was an instant juggernaut. His ability to control multiple bodies was unique, as was his control of gravity. There were just so many moments during his fight with Naruto that were so cool due to his abilities, especially the Chibaku Tensei.
3 Obito: How Long He'd Been Pulling Strings
Obito being behind so many things from the past instantly puts him in mastermind territory. From working with Danzo to posing as the Mizukage to his battle with Minato. They all set him up as a final boss level villain, one that eventually gave way to the true mastermind in Madara. For a while there it seemed like he had his hand in just about every single event in Naruto's history, as involved as Naraku was in Inuyasha or Aizen in Bleach.
2 Pain: Leading Akatsuki
Yes, Obito ended up being the true leader as Tobi, but Pain was the one actively calling the shots as far as anyone else was concerned. He was easily the strongest in the organization as well, one well aware of Obito's abilities and probably would have been able to end him if it came to it. At least if Tobi's battle with Konan was any indication. Regardless of how that fight would turn out, Akatsuki was the biggest enemy force Naruto had to deal with throughout the series.
1 Obito: Identity Reveal
Obito's reveal as Tobi wasn't groundbreaking as many expected him to be the man behind the mask. That's not the one we are talking about, however, it's the one where Tobi was no longer the goofball he was played up to be. Tobi taking on a more serious tone was one of the most surprising moments in the whole series. Even his reveal as Obito had a major impact on the characters, even if it didn't have the same shock value to the readers.