glojo,
To reply to some of your questions:
Who decided to opt for the STOVL version when it is technically a far more complex aircraft which would demand more servicing, less air time.' - Not sure where you get the less air time bit from.
Has one more engine.' - As has been already stated, it doesn't have one more engine, it has a lift fan. i.e. basically a large 2-stage compressor.
'Smaller bomb bay which means it is incapable of carrying some of our larger air to ground munitions.' - Which UK large air-ground munitions are you talking about? The STOVL can carry the UK's Paveway IV very comfortably which is all we're going to try to put in the bay of the -C. The -B will be able to carry the same number of Small Diameter Bombs in its bays as the -C, which 9 days out of 10 is a far more relevant comparison than the number of 2000lb JDAMs (which the UK do not have in their inventory).
'Has to ditch ordinance prior to its vertical landing envelope.' - No it doesn't. The specification of the -B requires it to be able to land vertically with full internal bays and fuel to wave-off the first approach and have another go.
'A very worrying potential of heat damage to the flight deck.' - This was not designed in intentionally but is something that is going to have to be managed. Then again the heat footprint of a -C in afterburner on a Nimitz jet blast deflector also causes concern and will have to be managed.
'Those are the benefits but on the downside it is a far more expensive aircraft that will only be built in limited numbers.' - Not sure which numbers you're looking at, but the current program has more -Bs being built than -Cs. And there's so much smoke and mirrors around the price are you sure that a -C is cheaper than a -B? They're pretty close in price as far as I know, and some ppt slides even show the -C to be more expensive to buy than a -B.
Also, landing the -B in STOVL is ridiculously easy. The training burden before you deploy your predominantly land-based sqns to the ship would be trivial. Landing a -C on a ship is not ridiculously easy at all and will require the pilots to train almost continuously if they are to maintain readiness to go to sea. The USN dedicate months of training to their F-18 sqns before they embark on a cruise and landing a -C is no easier than landing an F-18.
The UK has no current air-air refueling solution for the carrier. It's not needed for STOVL aircraft, but other Navies use it (rely on it?) for conventional carrier aircraft e.g. Super Hornet for USN, Etendard for French etc. Buying the -C means the UK now has to figure out and pay for solving that problem.
But we're drifting way off thread now, sorry. Regards,
Single Seat, Single Engine, The Only Way To Fly