The ninja clans have misgivings over Hiruzen's refusal to train the Kyuubi jinchuuriki, but are willing to let it slide. However, when the grades for Naruto's first year of Academy are revealed, they're appalled to see what an utter dunce he is! They beseech Hiruzen to give special training to him, since he obviously isn't progressing in the Academy—but Hiruzen refuses to treat Naruto differently.
To rectify this error, the Ino-Shika-Chou clans decide to use a Yamanaka forbidden ninjutsu—Mind-Body Merge—that allows one mind to control two bodies tracelessly and permanently, replacing the target body's original host. After a year of training (on "missing" prisoners, with a non-permanent variant of the technique), Ino executes the technique on Naruto, and takes permanent control of his body without a hitch.
I don't know where the story would go from there.
Why hasn't Mind-Body Merge been used more often by Leaf or by the Yamanaka? Option 1: The technique has severe diminishing returns, since a linkage must be established between each pair of bodies (not just from each body to the bodiless mind). If more than two bodies are united under a single mind, the intelligence of the resultant hive mind (relative to the number of bodies under its control) starts to drop precipitously due to the extra load. (For example, a hive of in control of a hundred bodies would be a lot smarter than a single person, but still wouldn't have nearly enough brainpower to control all those bodies, of which most would require constant maintenance by people outside the system. There also are some slight distance-related effects that preclude keeping a spare body or two at home for extra brainpower while a primary body takes the field.) The Yamanaka don't think that the improved effectiveness of two-body hive minds is worth the stigma and reprisals that using forbidden techniques to permanently hijack the bodies of prisoners would bring on Leaf in general and the Yamanaka in particular. While the Yamanaka's penchant for temporarily hijacking the bodies of their enemies is widely known, knowledge of the existence of this permanent technique has not spread beyond the biggest of the Ino-Shika-Chou bigwigs—not to any of the Hokage, and not even to Danzou.
Why hasn't Mind-Body Merge been used more often by Leaf or by the Yamanaka? Option 2: A ninja's chakra is generated in equal proportion from his body and from his soul. Mind-Body Merge has one soul in control of multiple bodies (and minds)—so, two bodies = three-fourths normal chakra for each body, three bodies = two-thirds normal chakra, four bodies = five-eighths, et cetera, tending toward a limit of one-half normal chakra for an infinitely-large MBM group. This isn't a problem for the Ino-Naruto merge: Naruto's body has extremely high chakra reserves due to the leaking Kyuubi chakra, so the loss of the chakra attributable to Naruto's soul isn't overly damaging.