Here's an extremely interesting and nasty thought.
ALL the Bijuu (not just Kyuubi) are replaced by the
Eight Phases and
Cubia from the
.hack series.
Cubia, being by far the most important of the nine 'programs' (it represents the Key of Twilight, or Twilight Bracelet), would replace Kyuubi, and he'd presumably give Naruto an ability akin to Data Drain.
One thing to note is that while whoever has Skeith sealed in him (probably Gaara, since Skeith is the first Phase) would have Data Drain too, since Cubia IS technically the Twilight Bracelet, its version would be a lot stronger.
The only real problem I have with it is to find a way for what amounts to data-composed monsters to materialize in the real world. But given how Megaman Battle Network did something similar (during the second game, the final area was merging with the Net), I think a suitable plot point can be made.
And note - it doesn't have to be The World in Naruto's world... given enough of a reality distortion (which is what the Cursed Wave essentially is, and that's why it can put real people in a coma), something from a neighbouring reality (that reality being The World, wedged between the .hack world and the Naruto one) can easily be thrown in the Elemental Countries.
Once out of The World, I'd figure the Phases would go uncontrollable, as they are cut off from Morganna and, without their original goal available anymore, they'd probably act erratically. Cue attacks on the Elemental Countries. And since they are mosnters made of data, Seal Arrays like the Shiki Fuuin are the only feasible way to contain them, really.
Anyway, that's the basic idea. Thoughts?