*Edit* - its been pointed out to me that the term plot hole here is incorrect, which I agree with, anyway still leave your thoughts to help clear up my confusion
Sage Mode
After we jump forward in time, Jiraiya is sent on a S Rank mission to find out what's up with pain and amegakure. He infiltrates Pain's stronghold, sneaks around in some ducts and stuff for a while, but is eventually discovered and has to defend himself from an enemy he knows basically nothing about and later turns out to be the antichrist himself. What's an old guy to do?
He reacts by initiating what we now know is called sage or sennin mode, where the users takes on the physical characteristics of a frog and they become super powered through the power of loving trees and grass and stuff. At this point Jiraiya is already well-known to be one of the most powerful dudes in the world, and he just somehow got more powerful by becoming more ugly. Weird trump card!
Why I think this makes no sense:
Correct me If i'm wrong, But before this sage mode was never even hinted at in the series. Not ever.
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"Sage what?"
Previously, we were lead to believe that Jiraiya was as powerful as he was because he was skilled in an obscure discipline and had decades of experience under his belt, which is pretty impressive in a world where you could die at any moment without the slightest hint that something is amiss. Sage mode basically makes these assumptions completely false: he wasn't considered powerful because he was a better fighter or because he's been around the block, he's powerful because he has a super secret shape shift ability that makes him a super powered amphibian.
This could very well have been possible
if Jiraiya hadn't been caught in no less than two conflicts where going into sage mode would have ended Naruto for good.
The first time was when he encountered Itachi and Kisame in a hotel. At the time he seemed worried about the outcome of the fight but he was still able to put two ridiculously powerful ninjas in a situation that forced them to flee without even considering the possibility of going into sage mode. He didn't go all sennin on they ass, merely finishing with 'Ninpou, Gamaguchi Shibari - summoning the stomach of a toad from Myobokuzan, because he evidently didn't feel threatened enough,
because if he did he would have completely ruined their faces and Sasuke's goal of beating his brother would be taken care right then and there. (let the jiraiya vs itachi battle ensue below, but I think my point still stands)
The second time was when
he and Tsunade fought Orochimaru in the Sannin battle, where enormous summoned creatures were stomping and slithering around the battlefield. At one point Jiraiya gets hand-to-hand with Orochimaru after sinking his snake summons into a swamp with 'Doton, Yomi Numa' but fails to win the day.
Again, if he had access to sage mode at this point then why didn't he use it? By all accounts he could have very easily beat the piss out of Orochimaru, back-handed Kabuto, and basically ended the major conflict of the story right there. If he failed in a big way that day Tsunade and Naruto would have been killed. Was that not good enough reason to use sage mode? (let the Orochimaru Edo BS vs Jiraiya start)
Actually, we all know why he didn't use sage mode on these two occasions: Kishi-san simply hadn't come up with it.
The Elemental Affinity Test
After the time skip it's pretty apparent that Naruto is still pretty lacking. Despite the fact that he spent three years in private training with one of the most powerful ninjas in the known world it turns out he's only any good when someone makes him go ballistic and he accidentally lets out the demon fox sealed in his body. All of the people he graduated to genin rank with, are now chuunin or higher (or jounin if you are exceptional like Shikamaru)
Naruto needed to be powered up. But how? Enter the elemental affinity test to my great frustration.
Basically, when you hold a special piece of paper it will react as if under the influence of one of the elements that apparently all ninjas are naturally aligned. If your elemental alignment is water the paper will dampen, if it's fire the paper will burn, etc. It turns out that Naruto was wind all this time and didn't even know it. And now that he does he can undergo some proper training and get that level up he needed to fight all these ridiculous ninjas around him.
What is my problem with this I hear you say?
Think back to the beginning of the manga/show to when Naruto and company were still in basic training. Remember when Kakashi went through all of the trouble of illustrating the fundamentals of ninja combat by using them on his students?
He was pretty serious about showing his students the ins and outs of being a murderer for hire, and presumably held back from actually trying to kill them because that's what the chuunin exam was for and he didn't want to ruin all the fun.
"So, we just get tagged out or something right? Right?"
So, why didn't he hand Naruto and his team these little pieces of paper in order to discern their elemental affinities right away to help him properly focus their training? The paper is clearly special somehow and maybe it's kinda rare or expensive but this seems pretty important. Why wouldn't teachers get this crucial information as early as possible? To save money? The trees? What? It makes no sense!
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The answer is, of course, that Kishi-san made this up way later in order to give him an excuse to power up the characters even more. If he thought this up on day one there there is zero reason for Naruto to not have known his alignment to wind from the first day of his genin training. Argh![/B]
Sorry if this has been posted before, just venting as usual. This is combination of research and reading other people's theories as well.