The C3I aspect of CV(F) is a very interesting example of "requirement creep". I understand from a former member of the Sub-Navy Board that the original intention was for the ships to be simply floating decks/ hangars with the vast majority of the combat power to be invested in the aircraft. C3I was supposed to be accomplished from the Type 45. The RN also had an aspiration that HMS Ark Royal would be retained in service and converted in to an RN equivalent of the USS Mount Whitney in order to provide a base for a JFHQ (Afloat) under a completely different operational requirement, with its own budget.
Obviously the Ark Royal plan never made it very far but the CV(F) indigenous C3I is a very expensive addition. The RN might have been better off sticking with the original floating airfield plan & buying the extra T45s with the money.