Naruto vs Pain told a much better story then Jiraiya's, IMO. Jiraiya vs Pain was another teacher vs corrupt student. It was good, don't get me wrong, but Pain's fight with Naruto was much better. More was on the line. Pain destroyed Konoha and at the time he was killing off characters left and right. Even Kakashi was presumed dead until the BS ending, which ruined how great the arc was. We also got to see nearly all of Pain's powers in the Naruto fight, as well as new powers from Naruto. The Pain Invasion arc actually felt like it could have been the climax of the series. Naruto had officially reached a Gokage level status at this point and Pain was a enemy with powers nobody else had at the time. It didn't feel like a rehash to me, only Pain's speeches.
The Sasori battle was good, if only because puppet style is such a rare treat and seeing Sasori with all these crazy powers and puppets was different. But beyond that, the fight's not that memorable for me. There are plenty of fights I'd put above that one. It's overlooked by I really loved the Sasuke vs Deidara battle. Deidara's C4 Bombs were outstanding. It's just to bad he was fighting Sasuke and his plotringan. But it was a good part 2 fight. Even the war arc, despite my overall dislike of it, has some very signature moments for lesser characters. Especially in the case for lesser characters like Choji and Ino.