Naruto as we know it is a lie.
Wow, talk about your confronting, controversial and easily-misunderstood opening statements.
But what I mean is that the series we are reading now is NOT the series Masashi Kishimoto originally planned on writing. I have no idea what he DID plan originally, or even if he HAD a plan for the long term, but the current ninja war over the bijuu and Madara's 'Moon's Eye Plan' is not it.
The shift happened after the timeship, although Kishimoto may have committed to the change of direction beforehand (maybe as early as the Tsunade arc, with the first appearance of Itachi and Kisame). This led to a massive, but surprisingly subtle, retcon to incorporate plot elements that simply did not exist before, or even contradicted earlier ones.
This is hardly unknown. Dragonball Z contradicted itself so many times that you could just shrug your shoulders and say "eh, whatever" every time Akira Toriyama rewrote half the backstory (anyone remember that the Saiyan's were originally equal partners of a race called the Arcosians who used them to conquer planets for resale, rather than oppressed and overshadowed flunkies of galactic overlord Frieza?). But Naruto takes itself rather more seriously, while DBZ goes completely over the top with every story arc, so while not as obvious, the retcons in Naruto are rather more jarring. Not that this thread is a criticism of the series, but I thought the retcon made for an interesting discussion point.
So let's break it down into the 2 key points for examination. Before the retcon:
1) the bijuu "series" and the concept of "jinchuuriki" did not exist.
2) Uchiha Madara and Akatsuki were not intended to be the main villain of the series.
1) The concept of "jinchuuriki" and the series of 9 "tailed beasts" was invented late into the story.
This one is actually surprisingly obvious. The current perception of the "bijuu" is that they are ninja weapons, used to create jinchuuriki and a disliked but accepted convention of the world of ninja. There are a series of 9 of them with differing numbers of tails relating to their power and they are all actually parts of a greater "10-tailed beast" that was sealed into the moon by the Sage of 6 Paths. The jinchuuriki of the Kyuubi before Naruto was his mother, Kushina.
This is obviously not how things were at the beginning of the story. The Kyuubi no Kitsune was a single powerful rogue demon which was imprisoned inside Naruto as an act of desperation by the 4th Hokage because it couldn't be killed. The Shukaku of the Sand sealed inside Gaara was NOT in any way related to the Kyuubi and was not even really a "demon" in the classical sense. And there sure as hell wasn't a full "series" of them.
Let's look at the evidence from the story pre-timeskip. The later story would have you believe that jinchuuriki are common and normal (for a given value of "normal") for ninja villages. People don't like or trust them and usually shun or even abuse them, but they're not some dark secret.
Now, if that were the case, why did the 3rd Hokage go to such lengths to make sure that no-one, not even Naruto himself, knew about the Kyuubi inside of him? Why, even once he was aware of its existence, did no-one ever take steps to teach him his role as a jinchuuriki or how to use the Kyuubi's power (not until Jiraiya taught him to start tapping the Kyuubi's chakra in chapter 91)? The word "jinchuuriki" wasn't even mentioned until after the timeskip and any time Naruto tapped the Kyuubi's power was treated with suspicion and fear rather than, y'know, what he should be doing.
Then there's Gaara, and here is the most obvious proof of the retcon. Once the timeskip had happened, the first arc revolved around Akatsuki kidnapping him to extract his "one-tailed beast". This was the first time it was stated that the Shukaku inside Gaara was the same kind of beast as the Kyuubi, while previously Gaara had been meant to be a foil for Naruto, his dark mirror rather than being literally the same as him. In chapter 97, Gaara blatantly explains the history of the Shukaku and himself- it was an incarnation of the sand itself, the living spirit of a Hidden Sand priest that had been sealed in a kettle. Naruto's realisation that "He's the same as me" was only meant to go as far as their backgrounds of isolation and loneliness because of the monsters sealed inside them, no more. Additionally, the nature of the Shukaku and its powers are TOTALLY different from the Kyuubi or ANY of the other bijuu introduced afterwards. It didn't give Gaara access to its massive chakra or have any form of chakra shroud. It gave him elemental control over sand and access to a number of sand "techniques", and it could create a giant sand simulacrum, totally different from the released form of the bijuu which transform the body of the host (while Gaara remained embedded in the forehead of the giant sand body). Gaara was also created as a "secret weapon" by a ritual which bound Shukaku to his body in his mother's womb, killing her. This was also seen as a radical and possibly forbidden experiment (which was considered to have FAILED), which hardly gels with the idea of jinchuuriki as common weapons used by the villages (contrast with the backstory of Killer Bee). While the Kyuubi was imprisoned inside Naruto, the Shukaku (despite supposedly being a much weaker creature than Kyuubi) possessed Gaara and tried to take control of his body whenever he slept (the dark rings around Gaara's eyes were originally indicative of his chronic insomnia rather than a "bijuu mark" like Naruto's whisker marks or Yugito's catlike eyes). While Gaara was originally created to be a character in a similar situation to Naruto, to show how he could have turned out if things had gone badly, that was where the similarities were meant to end.
So why did Kishimoto do this? Come the timeskip, Akatsuki needed a plan. The obvious choice was the Kyuubi- it had been portrayed as the most powerful creature in the story so far, it was what made Naruto unique and defined half of his character, so what could be more interesting than having them wanting it for some neferious purpose? We already knew they had their sights set on Naruto from Itachi and Kisame's first appearance in the Tsunade arc, but obviously they couldn't be going after him ALL the time or the story would simply get bogged down with "Akatsuki try to capture Naruto>they fail" (since succeeding would have been out of the question). Bring on the bijuu; suddenly there's nine of these things for Akatsuki to go after- and unlike with Naruto, they're allowed to succeed without derailing the entire story. Hell, it even allowed Kishimoto to involve Gaara in the first post-time skip arc, to raise the personal stakes. This led to bigger and more epic things until we ended up where we are today.
Of course, that raises the OTHER big issue:
2) Akatsuki and Madara were created out of nothing.
Before the first appearance of Itachi and Kisame in chapter 140, who would you say was the main antagonist of the series? Orochimaru, right? Well duh- he'd just killed the 3rd Hokage, arguably the biggest and most shocking twist in the plot so far. Even to this very day, the 3rd is the most significant non-antagonist character to die in the entire series (slightly ahead of Jiraiya). Orochimaru had also orchestrated the entire war between Konoha and Suna by murdering and replacing the Kazekage, he was considered a legend together with Jiraiya and Tsunade, he was incredibly creepy and he wanted to steal the body of Sasuke, the protagonist's best friend, making it personal between him and Naruto. He had "Big Bad" written all over him. From chapters 45 (his first appearance) to 238 (the start of the timeskip) the plot basically revolved around him. Even though the Tsunade arc was about bringing Tsunade back to Konoha to become Hokage and to heal Sasuke, Kakashi and Lee, and was the debut of Akatsuki, the antagonist of the arc ended up being Orochimaru again.
Fast forward to the post-timeskip story. Apart from a fairly memorable appearance in the Grass Country arc (starting from chapter 289) his role is to get beaten up and absorbed by Sasuke, then make a sudden shocking and unexpected appearance in chapter 392 in the fight between Sasuke and Itachi, only to get instantly beaten and sealed forever. Wow, talk about anticlimactic. This CANNOT have been planned, otherwise Orochimaru wouldn't have been built up as such an awesome villain in the first half only to become such a loser punk in the second.
So, why was Orochimaru beaten so pathetically? 2 reasons. First, while he was a great villain and his interest in Sasuke made it personal for Naruto, he clearly had no interest whatsoever in the Kyuubi. Since the Kyuubi and the newly-introduced bijuu were going to be the focus of the plot post-timeskip, Orochimaru could sadly no longer serve as series Big Bad. Akatsuki gave Kishimoto an entire LEAGUE of Orochimaru-level guys to use as antagonists, especially once he revealed Orochimaru was an ex-member. It was all about scaling the "epicness level" of the plot up. Unfortunately, this made Orochimaru either a loose end or even an outright distraction from the plot, so he had to be offed.
Second, let's look at HOW he went down. First he gets utterly pwned by Sasuke. Then he gets pwned even MORE by Itachi. Is there a connection? You bet- the Uchiha Plot Stranglehold Technique. To use Troper terminology Orochimaru got utterly Worfed to show how awesome and powerful the Uchiha's are, and I think you can see where this is leading...
Enter Uchiha Madara. Madara was first mentioned offhand in chapter 309 by the Kyuubi as someone who could suppress the power the of the bijuu. Many fans cried foul when comic relief clown Tobi was revealed to be long-dead master Uchiha and the REAL leader of Akatsuki, but that's where the money was. With a plot revolving around jinchuuriki (who had to be plausibly strong for this plot to make sense), Kishimoto needed an antagonist who could convincingly be considered more powerful than them. Itachi couldn't be the villain, he was too personally connected to Sasuke and if he became the series' main villain it'd be stupid for Sasuke to remain antagonistic towards Naruto and co (and the revelation that he's really a good guy who's loyal to Konoha would also become impossible). Madara fit the bill, even if using him was a total Ass Pull.
What does this boil down to? Uchiha Madara was made the main antagonist of the series, despite it making very little sense and seeming to come out of nowhere, because he was the antagonist Kishimoto needed to keep the plot moving. Pain wouldn't do- Kishimoto wanted to make him sympathetic. He didn't create Akatsuki's plot, Akatsuki's plot (and the manga's plot) created him.
Besides, look at Akatsuki in general. Their first appearance was in chapter 140 where Itachi revealed they wanted Naruto for reasons unknown bt obviously related to the Kyuubi. Then we get told their plan is to use the bijuu to become the most powerful ninja organisation in the world, eclipsing the great villages and basically making them de facto rulers of the world through economics. Then Pain reveals he wants to create an immense bijuu WMD to scare the world into peace. Then Madara trots out his stupid 'Moon's Eye plan' and all bets are off.
Does this sound like it was planned from the beginning? Hell no. The details of Akatsuki were practically being made up on the fly. Look at the rings, for example- they were initially portrayed as extremely significant (Orochimaru kept his on his severed and decaying hand, Tobi figured he could join the leadership of Akatsuki when he found Sasori's ring etc) but were subsequently COMPLETELY forgotten and never mentioned again.
In short, Akatsuki was originally created as a vague "evil organisation" Kishimoto could use for whatever plot he thought up as he went along and Madara was the final result of this. Orochimaru was meant to be the original villain of Naruto, but when he reached his limits as an antagonist he was mercilessly axed.
I hope you found this post interesting and thought-provoking. One can't help but wonder what direction Masashi Kishimoto INITIATLLY planned on taking the series in? Hell, in the initial pilot chapter Naruto was an actual kitsune in human form who lived in a modern world without even so much as a mention of ninjas!
TL;DR: Go back and read it you slacker!