The reasons are outlined in a Warships IFR of April 2018. The piece is written by Graham Edmonds “How to Avoid a Clash of Cultures and Operational Needs Hampering UK Carriers”
As background info I understand the plan is to standup 2 x FAA Sqdns and 2 RAF.
I’m unable to link however in summary:
Pilot currency in operating from carriers is vital and were RAF Sqdns not to routinely embark major deficiencies will occur because currency requires not only operational flying from the carrier but also equal time in a simulator.
In the Joint Force Harrier time statistics show that RAF embarkation time in carriers were low.
This not only effects pilots but ground crews also.
The on watch off watch embarkation plan between the four squadrons raises further operational and administrative differences, flying from sea operates from a different set of rules. There are no diversion airfields, the airfield/carrier is not in the same place from take off to landing and the scenery is unrelentingly unchanging.
Harmony rules differ between the services. RN personnel can be separated from home for up to 9 months, the RAF from between 3 & 4 months.
A question in the House of Lords enquired if Harmony rules for RAF persons serving in the new squadrons will be brought into line with the RN, answer, RAF Harmony rules will apply.
This lack of joint ness means that in a carrier deployment of 9months the embarked RAF chaps could be changed mid deployment at least once even twice.
This undermines the maintenance of operational capability, in the Harrier days RAF pilots on 3 month detachments rarely achieved a night flyingcapability, in the final years of the last Ark Royal’s strike carrier deployments the number of RAF pilots who qualified for Full Weather operations was very low if not nil.
Under these rules a surge to three embarked squadrons and then to be fully qualified is almost impossible without lengthy qualifying periods beyond the present administrative rules.
The shortcomings become readily apparent when the facts are laid bare.
Probably worth recalling that the Harriers were largely committed to Afghanistan during much of that period. - which leaves you with a choice - do you demand the RAF park cabs on deck on ships well away from anything interesting while the rest of the UK is massively involved in a war of counter terrorism against a land locked country?
What (in those circumstances) was more important? Having pilots current in deck ops on a carrier or available to strike targets endangering troops in contact?
I think some of this will be fixed if the FAA expand with time to a fully established carrier based fast jet culture - for many decades, much of the FAA's structure has been filled out by RAF pilots in FAA jets or roles (and indeed, two of the highest scoring pilots in the FI were RAF)
Additionally, much of the support for the Harriers were RAF technicians - they'd done the courses, were familiar with the jets and could keep 'em flying.
If the FAA are funded to increase in sizes significantly, we may see a change - riight now, we're at that strange situation where the RAF underpin much of the day to to day flying ops of the FAA, and are complained at for it. I suspect the solution is to accept that the FAA and RAF will have to work hand in hand to provide for the security of the country, and from what I understand it, for currently serving RAF and FAA, this isn't total anathema.
It's a purple force, staffed with people who at the heart of it, wanted to serve their country - I suspect it'll work itself out.