BlastX
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Well I think it's also because once he befriended Kurama he's the one that gathers Natural Energy inside of Naruto basically what the Toad Sages were to Jiraiya (and it's even explicitly compared) so Naruto has practically unlimited Sage Mode now so he can use with much more freedom than before.another interpretation you can have is that its less that sage mode got stronger and more than Naruto wasnt as experienced with the form so its basically a nerfed sage mode in the pain arc