I think that Nikon tries to move the entire line up to camera bodies without build in AF engines. They will keep the AF engine in the pro and semi-pro bodies for the next generations, but the consumer lineup won't get the AF engine.Thus, actually, the DX line will go back to the earlier times of 3 body lines: D50, D70, D200. Now, D3xxx, D5xxx, D7xxx. Then it's clear D5xxx line will be upscaled to a D90's body level, like D7xxx is moving up to Dxxx line level.
I think the successor of the D5000 will indeed be moved up a bit to the place of the D90, but without AF engine. All new camera models get more features that move them closer to the current next model (D5000 -> D90....) and slightly higher prices while still being cheaper than the current higher level body (D5100 slightly cheaper than D90).
The D400 successor will probably be a FX camera, slightly below the D700 (features and price) while the the D800 gets more features and a higher price.
Looking at the recent price trends Nikon raises the prices of the gear. They can't just increase the prices for the cameras because the cameras have certain price slots they are in, but if Nikon basically creates a new camera line up they can position the models the way they want and increase the prices.
In short: every model gets moved up a bit without replacing the model one step higher in the line up. This way the low end makes room for the mirror less system and the AF engine becomes a feature of the higher end bodies.
I think Nikon can get away with this if the replacement models offer enough to get the customers think about how many AF-D lenses thy have and if the newer AF-S lenses aren't better...
Disclaimer: I think it's a bad idea to remove the AF engine. I'm just trying to guess what Nikon will do. I do think that with a good AF-S lens line up for DX the need for an in camer AF engine is small for most or many customers.