What we have here is a confluence of two programmes that have been linked, probably shouldn't have been, but for a number of co-incidental reasons are inextricably intertwined.
Once upon a time, there was a Common Affordable Lightweight Fighter, which then turned into a STOVL Strikefighter, which also turned into Joint Affordable Strike Technology. That beast was supposed to replace the A10, AV8B, F16 and (implicitly) the A6. Some thought it would also replace the F14. By virtue of part of it being STOVL it also got the prime position replacing the SHAR (and IT/SP AV8). Today we call that beast F35 A, B and C.
Once upon a time there was also a ship called CVSG(R). Then it became CV(R) and in around about 1998 it became CVF. There is a reason that the (R), became an F and that was the realisation (and endorsement) that the UK didn't need a replacement ASW helicopter carrier with the ability to carry a limited number of f/w aircraft. What it needed was a maritime capability to provide both f/w Fleet Air Defence and deployable strike capability for expeditionary warfare. The requirement for Fleet AD has not gone away (despite the enforced capability holiday on retirement of SHAR) and is complementary to delivery of Strike (one set of support facilities, crew etc). That means a substantially bigger ship than CVS, which led inexorably to CVF. The difference in size between CVS and CVF is partly a consequence of this, but also due to correcting the inherent limitations of the CVS design. However, despite size not being proportional to cost, the difference between CVS and CVF/QEC has been used as a stick to beat the project with on a purely subjective basis for the last 10+ years. Shrinking the design has been looked at, but gave little cost saving for a significant loss in capability. It did lead to significant delay and consequent cost escalation.
Once CVF/QEC became the size it is, it might have been more sensible to divorce aircraft choice from type of operation. That stage was probably reached in 2004 when a decision could have been made to go with FA18 or Rafale and get a 5th gen aircraft later. Trouble was, EMALS was seen as very risky at that stage and steam cats as undesirable (manpower heavy, likely to be replaced), so the STOVL comfort blanket looked safer, particularly once JFH formed. On top of all this was the absolute refusal of anyone in MoD to commit to carriers (largely based on the "size" perception, combined with the F35 cost profile), which led to significant cost escalation in the ships through delay.
Only later, as F35B struggled, did F35C start looking more attractive, but still EMALS was "high-risk" until fairly recently. Trouble was, F35C then starts to experience issues, just as EMALS began to deliver. However, EMALS is still likely to offer the best long-term option, particularly when you consider that a successor STOVL aircraft to F35B is highly unlikely (one of the reasons the adaptable CVF design was proposed in the first place).
So here we are, apparently about to make a (wrong imho) decision to follow a blind alley for short-term cost saving reasons. I have been particularly critical of the MoD (but mainly The Great Financial Genius - Cyclops) in terms of the decisions made - or more precisely, the decision to avoid decisions. That vacillation has led to the ship project (though should more precisley be the both ship and aircraft projects) gaining a reputation for being a basket case. I stand by those criticisms, but in fairness, there has been a confluence of competing risks that have been difficult to balance. Doesn't excuse the failure to sh1t or get off the pot, but does illustrate the potential for unsightly skidmarks.
Finally, to echo Engines - whatever happens with F35, getting a STOVL aircraft to sea for what will probably be only the third distict type operationally in fifty years is no mean achievement. That (and the other elements in the wider programme) deserve respect technically, whatever one thinks about the wider programme management.