...so continues the eternal debate... and quickest way to wind up anyone wearing light blue...
Now that the liklihood of a proper air war occuring (the occasional foray by the russians into UK airspace but a distraction) has shrunk to almost nil, the RAF will now, in almost every likely scenario, always be acting in support of one of the other two lead services. The only exception really being a response to a 9/11 hijack scenario.
So, to that end, to ameliorate many of the single service integration issues of procedures, IT systems et al, there would be some sense from the operational perspective of giving the toys over to the direct control of the other two services.
Realistically, however, many assets would be equally desirable to both "surviving" services - Air Refuelling, Surveillance, UAV to name a few, offering questionable interoperability advantages, the admin and maintenance would still need to be done and there would no doubt be significant morale and esprit-de-corps erosion through forcing people to change cap badge.
Tuppence worth from me.