Is our employment of our first 5th generation, LO platform going to be dictated by where we happen to land, or what we do while airborne?
If the former, then the RN would seem to have an argument. Personally, I think the latter is far more important, especially as most of the scenarios the UK is likely to get involved in would involve operating from land bases. Due to the inherent limitations of carrier ops, land basing allows much more effective generation of air power capability. Lightning II should therefore be operated by this country's professional air power experts - the RAF. Even the USN admit that the USAF are far more effective than themselves at employing air power.
However, as has been mentioned, the USN have enough mass to justify their own specialist fixed wing air arm. In this era of financial austerity, can we really justify keeping a fixed wing FAA, with its own structures and overheads, to man 42% of a single FJ squadron?