From what I heard during sea trials the launch cycle of the Merlin takes so long that it is incompatable with the launch cycle of the Harrier.
Not quite true. It is actually quite quick off the deck when it is fully serviceable. I think the reason for putting them on the RFA's is to do with space, if the CVS has a full complement of FA2/GR7/SKW.
There has always been issues with operating fixed and rotary assets off the same deck. Any U/S helo stuck on the spot (for example unable to fold the rotors) is going to screw up the FW programme.
Plus the RFA's are a lot nicer to live on !!