I feel like tracing everything back to one mastermind cheapens most stories and makes the world flat. ANyone else?
I disagree, but that is mostly because, from a thematic and stylistic point of view, I like the concept of "The devil" in fiction. By that concept I mean: The evil mastermind that from the shadows manipulates the negative emotions, feelings, thoughts, temptations and ambitions
already present in human beings, then exacerbates them and uses them to further his own goals. He may not neccesarily be the "seed of evil" per se, as "doing evil" is a natural condition of the human being (just like the capacity for "doing good"), but precisely because he has a great understanding of the human nature, he can manipulate and benefit from the darkest aspects of it with mastery. For me, that kind of thing makes for an excellent villain and an excellent conflict for a story.
Now, Mr. Rigger has a point in that too many writters fail at doing this "central evil mastermind" properly (retcons and "arc whelding" are certainly the most common reasons), but
there are stories that have actually done it in excellent ways (Full Metal Alchemist in any of its variants inmediatly comes to my mind).
As to Naruto, one of the reasons why I like the character of Madara so much is because I believe he is a very effective "devil" (Orochimaru was another excellent "devil" by the way, but certain elements of his character were always repelent to me, though that is a discussion for another ocassion). Of course, I agree that the overall Akatsuki plot was not done as well as it could have been done, and the execution has been very sloppy at times. But I don't think it's a matter of the retcons or lack of foreshadowing, rather I believe said problems are more a result of what may actually have happened: What Tsuki mentions about Kishimoto changing concepts. Looking at some of the early volumes of part II, it seems to me that Kishimoto had already planned a certain plotline for the Akatsuki but something happened and he changed his mind (look at the "original" plan that Pain originally told to Hidan and Kakuzu and compare it to what he told to Jiraiya, then compare that with what turned out to be Madara's actual plan).
Nevertheless, on principle and in theory, I think the overall idea of a shadowy organization and its nefarious leader seeding and manipulating the conflicts already present in the Ninja world with the aim of using the bijuu to conquer the world, can make for an excellent story. I even think the "Moon's eye plan" can work well as a plot. Overall I don't think canon Naruto is as bad as many people paint it, I just think it needs refinement (a lot in certain areas, less in others).
Now, I personally believe that at the end of part I, Kishimoto already had in mind (if not properly or completely defined) that an Uchiha was going to be the leader of the Akatsuki and the major enemy of the series. There are four hints of it. Two have already been mentioned: The statues at the valley of the end and the mention by Itachi of the Third Mangekyo user. The third (and the more critical one, IMO) is what Itachi says to Sasuke about looking in the shrine for the scroll with the secret about the true purpose of the Sharingan and the Uchiha clan. That is the first time that the "accursed blood" of the Uchiha clan and their connection to the Kyuubi it's mentioned (and then, the second arc of part II is the first time that the name of Madara is mentioned by the Kyuubi itself). The fourth it's the simple fact that Zetsu (who at the beginning of part II was explained to be the scout of the Akatsuki) was an expectator of the fight between Naruto and Sasuke, hinting that the organization was not only interested in Naruto but in Sasuke as well.
It seems to me that, originally, the shadowy figure with the "strange eyes" that knew a lot about Konoha and the way the ninja world worked, and that was only referred as "the Akatsuki leader" (and who eventually became the character we now know as Nagato/Pain) was originally going to be Madara (indeed, while "the 4th Hokage is the Akatsuki leader" was a very common theory back then, I do remember a couple of forums where "Madara Uchiha is the Akatsuki leader" was mentioned). It's also possible that Tobi was going to be something really sinister (if not neccessarily at the level it got) from the beginning, by what Tsuki mentions, by the fact that he did was introduced with captions that hinted at something ominous, and by the fact that, even if the character was portrayed as a buffoon, it was just easy to suspect there was something up with him given the other members of the organization as well as his own appearance (to be among such group of psychos and freaks, there
had to be something really sinister behind that mask and armor).
Of course, given what I have mentioned previously (that I believe the Akatsuki plotline was changed from the original plan), I suppose that at some point Kishimoto decided that "shadowy figure = Madara" didn't have enough impact and changed it for "Tobi = Madara".