It's Unlikely that Jiraiya Neglected Naruto's Base Form During Their Training

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When we saw Naruto and Jiraiya's first training session with one another, Jiraiya's goal was to train Naruto to use Kyuubi's chakra, a weapon necessary to performing the ninjutsu he was trying to teach him, Kuchiyose no jutsu. "Anyway...this special chakra that only you have will become your greatest weapon. It'd be a waste not to use it!" This line that Jiraiya said is key, because Kyuubi's been a constant throughout most of the series. Naruto has indeed used this weapon to his great advantage. Also, up until recently, we saw that every time Kyuubi's helped him without having any visible negative effects. It was established from the beginning what Jiraiya was trying to do with Naruto. Fast forward to Akatsuki coming into the picture. From Jiraiya's knowledge of a group full of S-Rank criminals, to the Konoha Jounin's and Jiraiya's separate encounters with Itachi/Kisame. Naturally, when we saw Itachi's power, it was extremely difficult to grasp the fact that there were eight other guys like him. Consequently, there was no way Naruto could actually compete with any of them as he was without getting killed. So what could Naruto do or use to be able to stand at least a small chance when fighting them? His greatest weapon, the Kyuubi, of course. Now the theme we pin to Jiraiya's goal and duty towards Naruto is "Protection", and the things Jiraiya's taught Naruto either had to do with Kyuubi directly (Kyuubi chakra training) or jutsu made possible and/or easier (Kuchiyose no jutsu; Rasengan) because of Kyuubi. That being said, it's not surprising that people would say that Jiraiya would almost exclusively teach Naruto things relating to Kyuubi and Naruto as a jinchuuriki over the time-skip. And people weren't far off in their presumptions at that point, since the first two Arcs of part 2 had to deal Kyuubi and Naruto. The first Arc dealing with jinchuuriki (Chiyo's explanation of jinchuuriki; Naruto/Gaara labels; revelations concerning Akatsuki's goals) and the second with the three and four tailed incidents. Also, Kabuto and Orochimaru have made comments about Naruto "developing nicely as a jinchuuriki", "Naruto becoming jinchuuriki-like", and Naruto's Kyuubi power growing ever-stronger, etc. People saying that Naruto was only trained to use Kyuubi were looking really good at that point. You see, I would've agreed with the general public's assertion of Jiraiya training Naruto only with using Kyuubi in mind to put himself more on equal ground with the likes of Akatsuki (and Orochimaru). I would've agreed with that assertion until we started seeing Kyuubi's tails, and Jiraiya's wary concern and fear of Naruto using any tails at all. These tails and Jiraiya's assessment of them changes my views on what Jiraiya actually did with Naruto during the time-skip. I bring the Jiraiya theme with Naruto back; "Protection". First, seemingly, he wanted Naruto to train with Kyuubi as much as possible to protect himself. By training Naruto in that mostly, Jiraiya's doing his job in protecting Naruto by, in turn, teaching him to protect himself using his greatest weapon as the sole shield against future powerful enemies out to kill him. With that in mind, it was a bit odd to see Jiraiya warn Kakashi against tailed Kyuubi use. Obviously, from Jiraiya's perspective, it was taboo for Naruto use Kyuubi chakra if it was to be in that chakra shrouded, tail form. We knew that the one-tail form rendered Naruto's arm useless during his fight with Sasuke at the Valley of the End. We knew that, but it seemed like Naruto kind of grew into that power. I didn't know; couldn't be too sure really since we'd only got a brief glance at the two-tail form. What we did see for certain, though, was Jiraiya warning Kakashi of Naruto's tailed form. As if he were protecting Naruto from Kyuubi or something. Why would Jiraiya warn others against the very thing that he seemed to be training Naruto in the most? What were the negative effects of the tail use? Would he lose his arm again? Does too much Kyuubi power put an immense strain on him? Does he go insane? Would that, in turn, make him hurt those close to him? Well, as we would later find out, yes...and more. Just being in the tailed form at all is constantly causing damage to his body. But once he goes to the fourth tail, he succumbs to pure destructive impulse, not even being able to tell friend apart from foe. By the time he reaches the fourth tail, he's covered entirely by a mixture of chakra and his own blood, and when it's all over with, he's able to heal rapidly through his internal Kyuubi chakra. And as we know from Shizune's explanation of the effects of Genesis Rebirth, and again going by Jiraiya's explanation, such rapid self-healing can shorten the users lifespan. So here we are now. Naruto has shown us to what extent he can go as a jinchuuriki, and it's turned out to be detrimental towards not only his own life, but also that of his comrades. Protection through use of Kyuubi is something Jiraiya obviously avoids now, despite it being the exact opposite before, seemingly, and he's told pretty much everyone who has needed to know about Naruto's Kyuubi issue. So now what else could Jiraiya have done to make Naruto stronger, yet without risking tails? See, from here the answer's rather easy: He trained him in his base form. Simple. After having experienced the wrath of Mini Kyuubi during the time skip, Jiraiya likely trained Naruto normally from then on after they both recovered from their injuries. The chances of Jiraiya continuing to train Naruto in using Kyuubi after that were very slim. But that, in no way, should stop Jiraiya from training Naruto's base form. Jiraiya could've limited Kyuubi's presence through some sealing method and trained him as a normal shinobi from then on. I mean, at some point, he did teach Naruto how to deal with genjutsu, so I'm positive he taught him things other than that and Kyuubi too. And as it would turn out, thanks to Kyuubi's chakra blending with his, Naruto's base chakra reserve is second to nearly no one, and with Kyuubi still there Naruto retains his abnormally high stamina. Given that, Jiraiya knows he can teach Naruto techniques that not many others could do due to the strength of his normal chakra reserve. It's not like Jiraiya's abstained from teaching base Naruto before. He, like all of us, has seen base Naruto perform the high chakra/stamina-taxing Kage Bunshin on his own, so he taught him another chakra/stamina-taxing move in Rasengan. Why would it be different over the time-skip? Answer: it shouldn't be and, now, likely wasn't. And, as it just so happens, out of the Sannin, we have never seen Jiraiya fight at full strength and show uber techniques and trump cards like Orochimaru and Tsunade. Maybe because Kishimoto wanted to let Naruto use them first and show us what Jiraiya's taught him? Also, now, with Yamato's speech to Naruto in 299 and having Naruto fight exclusively in his base form, I'm certain that Jiraiya's trained him like one would a normal shinobi. Fortify his base form (which continues to grow stronger with Kyuubi there anyway) with low risk of Naruto going on another rampage. Simple logic. After all that's happened, to say that Jiraiya hasn't trained Naruto in his base form at all would be rather foolish. And Jiraiya would have been foolish to continue that specific kind of training. After all, he realized that pushing Naruto to his jinchuuriki limits would ultimately kill Naruto, maybe himself, and maybe even innocent people around them; so he must have also realized that training him to the limits as a shinobi not only strengthens him but carries considerbale less amount of something disastrous happening. So, while normal shinobi training is dangerous too, it doesn't nearly carry the same level of risk as that of Naruto's jinchuuriki training.