Flying from the sea is not just about a few pilots doing deck landings, it is about an ethos and culture that wants to fly from the sea (aircrew, engineers, ATCOs, navigators (navy), chockheads, support structures, standards, SOPs etc etc).
Agree Pheasant and although the RAF may lack a "want" to be at sea, vice the RN's "A day not at sea is a day wasted" mentality, I would suggest that what is important, over and above the more spiritual aspects you mention (ethos and want), is knowledge, experience and [relative] currency in all aspects of flying from a carrier. Furthermore I argue that proficiency in these 3 areas is pretty evenly spread across JFH right now, with absolutely no uniform colour involved in the equation whatsoever - the parity is directly attributable to the RN's decision to scrap the SHar and a subsequent loss of people (culture/ethos/knowledge et al)unwilling to move to Rutland.
Simply put, the RN hemorrhaged people after the SHar's demise, it now doesn't have the numbers to man two GR9 squadrons' worth of FE and things aren't on the up. Assuming the RN stand-up their JCA Sqn after 2015 do you think that bolt-holing Valley graduates into F/A-18 jobs to maintain FJ stats is fostering the ethos and culture of being at sea that your refer to? I think not....