Of course noone really understands the finances for this but on the assumption that the amount of cash allocated to buy (and maintain) aircraft remains constant, this clearly means that we will get fewer, less capable (ref: dstl) aircraft. This is a big negative.
On the other hand it does mean they can operate off both carriers (assuming the mothballing plan is, err, mothballed). This is a big positive.
Unfortunatley the carriers are now limited to VSTOL/rotary, probably for their entire lives. A big negative.
Although it might appear more attractive now to go for a split buy (A and C) for RAF and RN, especially given the CEPP plan to only have 12 JSF embarked, I think it would be a mistake, denying us the ability to surge in crisis a la Falklands, although it must be a very tempting option for the RAF.