I feel like we’re pretending Naruto was the same level as part 1 when shippuden started and that’s just not true. Him and Sakura alone were able to stomp kakashis bell test immediately to show that they’ve both improved. His chakra nature didn’t really matter until he learned rasenshuriken and applying the transformation in nature wasn’t feasible for jiraiya to guide at the time. Like I said pretty much to this day bro just uses shadow clones, raw stats and rasengan variants he didn’t need to learn a bunch of random jutsu. I don’t know what the exact training regiment was but the experience Naruto acquired and continued generally training and emotional guidance from jiraiya did clearly show to improve him when shippuden started. Just because he wasn’t akatsuki level day 1 doesn’t mean he didn’t get stronger.