Glojo - it's not often I'm roused to be rude, but in this case, despite your background in naval aviation, you need to dismount from your high horse, sharpish.
If you read through the evidence in the report (particularly the sessions) it is clear that no-one is really interested in probing what the actual costs to convert PoW comprised. Unsurprisingly, they are relatively easily fobbed off as soon as someone mentions changing lots of compartments. You'll note they don't get into what those changes actually were......or the "factors" that meant the publically available costs for the USN EMALS/EARS systems suddenly became much more expensive.
There is no such thing as an "easy" conversion where you just "drop-in" EMALS and EAR (or Mk13-3 and Mk 7 Mod 4 for that matter). The designers were perfectly well aware that SHAR was being scrapped and that a STOVL ship was inexorably tied to F35B. Unfortunately for you and them, they were in no position to change the contracted design to accommodate this knowledge, when the customer (the Equipment Capability community in Main Building and to a lesser degree the JCA IPT) were proceeding on a STOVL assumption. The Alliance are
contracted to build the design requested by their customer. The later you change requirements, the more it is going to cost.
It remains perfectly possible to fit EMALS (and EAR) to both QE and PoW. They are designed with sufficient space and margins to receive those systems.
What the contract does not (and never did) include was the actual detailed design to system level (ie the actual structural seatings, cutting plans, weld procedures, cabling and power management system software) and subsequent supply of the hardware.
For a variety of reasons (some credible, some less so) the "cost of modification" (which may or may not include other elements) for one ship was "estimated" this time last year at £1.9Bn which exceeded what MoD was prepared to pay. As a contrast, you're not talking here about the sort of work required to convert Victorious, Ark or Eagle in the fifties. There are no major additions required to the flightdeck structure, there is no need reduce the ship to the hangar deck and start again. There almost certainly will be a need to put structural channels and seatings for EMALS on the port bow and the waist, empty the compartments on two deck for both those areas and where the EARS system is required and run some hefty cabling in the vicinity. there will also be quite a bit of software development for the power management system on the ship. As ship conversions go, that is relatively easy and would certainly not have been possible on something much smaller.
The real problem is that the Equipment Capability customer in town started with the assumption that STOVL was the way forward and that view never really changed. CTOL was maintained only as a fallback in the event that JSF STOVL either did not meet the performance requirement or was canned. All sorts of esoteric discussions trying to balance range of one variant against numbers of the other took place. All were irrelevant.
Neither the RN nor the RAF actually wanted to face the implications of what a CTOL force and the associated structure meant. The RAF feared (correctly) that to make a CTOL force work correctly, that a larger FAA would be necessary or the RAF would need to dedicate itself to going to sea on a more frequent basis. One meant giving up budget share, the other meant giving up OPCON of a sizeable chunk of it's force structure. Hence the rumour campaign typified by Wrathmonks comment above, suggesting that the RN just wanted a big ship - hinting that it was the size of the ship that was the problem, rather than the inferred change of role.
"If only they'd stuck to smaller ships like CVS everything would have been alright", which conveniently ignores the fact that smaller ships would not have been substantially cheaper and would have been even more hostage to the aircraft choice.
The RN feared (also correctly) that it would have to fight an attritional battle to secure that budget change, which it didn't have the stomach for, leaving the possibility of having to fund a larger FAA from the same share of the pie. This at a time when most of the RN was in need of replacement (Astute, T26 and to a lesser extent T45), when the RAF already had it's primary programme (Typhoon) in place. It is also entirely fair to suggest that there was a lack of understanding of how all the capabilities fit together to make the whole at senior RN levels (see transmogrification of MASC to Crowsnest for details). The last 1SL did not help himself with the remarks attributed to him regarding who was to fly off the ship. Bizarrely enough he was trying to make the joint case, but showed complete lack of understanding of the organisational consequences for his own team and others.
It's not a conspiracy by RAF or RN. It is a simple failure to balance competing vested interests. When contracted for (2007) the army was screaming for helos on Herrick, could not get as much as it wanted due to both deficient budgets for operations and entire fleets (Merlin HC3, Puma, SK4) that were unable to help due to either commitment elsewhere or unsuitability. Unsurprisngly, they looked at the RAF/RN CDEL lines with some jealousy and demanded their share. It's a brave man (RN or RAF) who would have demanded cuts in the army budgets at the time to pay for CTOL carriers. Hence STOVL was the assumption, right up until the press regarding Dave B began to get cancellation-serious. Then the brainwave for going to C, which was fine right up until the same long-term organisational and budget implications came out again. Then back to B.
The upshot is this.
Two ships are in build and progressing well. They are certainly not massively expensive by carrier standards (the latest USN CVN is running at $11Bn), but people like their expensive white elephant myths.
They will cost more than they should have, but this is largely a result of failure to commit to contract earlier and the paralysis of the 2003-2007 period, coupled with the ludicrous ISD slippage of 2008 that cost the best part of £1Bn (20% of total) alone. By that measure the B-C-B reversion is chump change. If you knock off the billion incurred by the ISD slippage, were getting two very capable ships for about £5Bn the pair - about $7.5Bn or $3.8Bn each for those who struggle to convert £ to $. Their manning costs will be hugely less than anything else of comparable capability - largely due to the size of their flightdeck.
Those ships will remain capable of embarking the best part of 40 cabs each, plus r/w - a capability that exceeds that of CVS by some distance. Good thing too as these learned gentlemen suggest (well worth reading overall).
House of Commons - Uncorrected Evidence - HC 1090-i
They won't have E2 and won't immediately have Crowsnest. There remains uncertainty as to how many fast jets we will eventually buy. AAR remains a concern. Only one may be in service.
However, much as we might all like a full-up F35C, E2, S3, F14, A6 etc etc airwing and we are not getting one, that does not make the ships valueless or white elephants. There is a huge amount of myth and legend surrounding their supposed deficiencies (see bastardeux's comment for details) - the reality is somewhat different.
Most importantly - over a fifty year lifespan we will be able to change them and they won't suddenly become irrevocably incapable of operating aircraft.
Perfect? No.
White elephants? No.
Great capability? - Depends on our collective ability to stick the course, which is not helped by over-dramatic wailing over what might have been, by implication suggesting that what is coming is worthless.