Heard this last night on NPR, that Negroponte sent out a letter introducing himself but also saying that in certain instances, CIA Station Chiefs should report directly to him!
Of course, the commentators immediately jumped on how this was another way of undermining the CIA's own internal command structure and that it would cause confusion, but I think that's the whole point. More below the fold.
As we all know, Negroponte has a history of being indirectly involved in what can only be called illegal activity (need we bring up Nicaragua and Death Squads?). But how this situation works out well for both Negroponte and Goss is plausible deniability.
If Station Chiefs need to run operations, and those operations receive their approval from either the CIA or the National Intelligence Director's Office, and one of those operations fails for whatever reason, both Goss and Negroponte can lay the blame on the other's organization without either of them taking any responsibility for it.
Admittedly, this is a pretty cynical scenario, but considering how this Admin works, I wouldn't put it past them. And given the lack of any real investigative journalism (for the most part), the story would fall through the cracks in a matter of days, if not hours.