I fully agree with you '5 Forward 6 Back', but thats not the way the inter-service politics game works.
You know as well as I do that if the RAF attempted to pass control of the Harrier over to the FAA fully the RN would scream blue murder because they can't (or more likely won't want to) take on the full cost of operating the force because it'd likely eat into the budgets for ships etc.
JFH has worked out better for the RN than the RAF. The RAF front most of the costs and the RN keep their toe in the FJ world but don't even need to fully man 'their' squadrons with RN personnel, why would they (the RN) want to change this?