OA,
Interesting couple of issues there.
If we are talking about an individual theatre then I'd have little issue with a Joint Force commander having overall operational command. The problem arises when naval assets are needed elsewhere. The thing about ships is they can move around the place and its often the case that the MoD will need to move ships around from one theatre to another to respond to events, or shift emphasis. If the JF Commander has deployed all his F35's ashore, where will the navy pick up extra F35's from?
Secondly, there are "real fights" and secondary theatres. Where F35's are needed for the "real" fight who is going to tell the secondary guy he can't have any air cover? Putting F35's ashore emasculates the RN- its like emptying a battleships magazines because the shells are needed elsewhere. Our £2bn worth of carrier becomes a useless liability.
The only sane answer to all this Treasury driven nonsense is to procure more aircraft- not enter a fantasy world in which- like cheap martial arts movies, the bad guys patiently line up to attack the good guy one after another.
Bin F35B, adapt Typhoon for CTOL and buy more of them, consider buying F35C in a decade or so as a "nice to have" for first day strike. In the meantime talk of ditching carriers to meet Treasury driven and wholley artificial monetary constraints (this isn't the 70's the UK is now the 5th wealthiest country in the world, no longer the "sick man of Europe" ) simply sets people who care about UK defence at each others throats and does Gordon Browns dirty work for him. The answer is a realistic defence settlement, not squabbling amongst ourselves.