Presumably the things put in place to train RN Pilots and others in CTOL operations will have to change now?
Not really. The guys and girls need to get used to big deck operations. Additionally the pilot programme on the F18 is about retaining (and growing back) FAA pilot numbers and gaining experience in maritime strike ops with the only navy that still does it properly. These people will be the LSOs, QFIs, QWIs, Senior Pilots and COs of the future. All things being equal (oh yeah!) the first F35 squadron should be manned by these new maritime aviators and not ex-Typhoon types.....but I won't hold my breath.