A recent release from Emirates left me with the impression that Emirates wants to eventually merge but they want FlyDubai to get itself in order and show a history of what kind of airline they are on their own before bringing them completely into a merger.
I know they are attempting to have FlyDubai use their narrow metal to operate the short or low demand routes and feed traffic into Emirates for long haul routes. They are also coordinating schedules for connections and trying to avoid directly competing in any way.
The whole situation seems odd, but I would guess it is a cultural divide that I don't fully grasp.
In short, it seems Emirates really wants to merge but doesn't approve of how the FlyDubai business has been run so they won't move forward with a merger until they are confident in the people and the organization. Just my opinion.
I thought the whole partnership was strange.