The main reason the RN is against CTOL ops for the CVF is cost, Catapults and arrestor gear are percieved not only as an extra installation cost but as requiring increased manpower to operate them (engineers). Basically it is a money issue, although the real price difference is most likely nowhere near as large as the politicians think and the navy's brass are frightened of rocking the boat. I would like to see CTOL CVFs personally, seeing as how we invented the steam catapult and the angled deck we should get our money's worth! It would also solve the MASC problem by allowing the E2 Hawkeye to join the FAA. This would bring cost savings by pooling training and support costs with the French which would go some of the way to compensate for the extra cost of CTOL ops, indeed training of F-35C pilots could be pooled with the USN (and the RAF could do likewise with the USAF if they adopt the F-35A).
I can see a row brewing about funding now that Blair has announced a replacement programme for the Vanguard class subs as the £20Billion they will cost is now supposed to come from the existing Naval budget, which is not much more than that to begin with! There also rumours of six more DDGs/FFGs being reduced to reserve (permanently) and type 45s being cut further. This is a ridiculous situation, you can't fight a war (two, Afganistan/Iraq) on a peacetime budget whilst blowing a fortune on Typhoons that have no guns and no threat to counter. We can afford more, the current defence expenditure is less than half what it was in the 80s (as a proportion of GDP) and we can't keep expecting the US to do it all for us, an unfair situation for America.