If memory serves the 'convertible' carrier was the original 300m and then 290m designs. The government then insisted on more budget cuts and forced a redesign to a smaller version, they then realised that that smaller craft had a poor sortie rate so forced another redesign up to the current 280m version. Along the way the ability to change launch systems was dropped which the government OK'd as it saved a few pennies.
So in brief, various governments introduced years of delays and cost increases due to constant re-design and engineering work while going about trying to save money in some of the most stupid ways possible.
At the height of the nonsense when the press and public was questioning what was going on the government of the day conviently forget it was them who changed the design brief and agreed to the dropping of various features.
Not quite.
The current design (design Delta) remains perfectly capable of being converted to catapult & arrester gear configuration. The general arrangement drawings for the ship show the space allocation for the systems quite clearly and you can see the spaces if you walk round the actual ship.
The problem is that once the arrangement drawings had been completed in 2004, no further detailed work on the CV design was contracted for, although the overall design config control was maintained. Essentially, while the design is capable of being converted, no-one asked the Alliance to actually progress the detail of that design (ie produce the detailed system and component level design information to allow people to actually produce the equipment items and install them on the ship). Part of that was reluctance (by the US) to release EMALS info to some degree because at that stage it didn't exist and also our favourite FLA - ITAR. But mainly because both RN and RAF were still treating the CV option as a potential fall-back rather than a serious option.
What that meant, was that when the CV-reversion was requested, production of the required design information would have meant either stopping work on the second ship and waiting for design info (while paying for the workforce, courtesy of TOBA) or progressing the ship but then tearing chunks of it out again to fit EMALS/EAR. That is why the projected cost is so high, when a rational look at the work content just to include those systems in the ship would never get anywhere near the £1.8Bn figure quoted.
So no design features were dropped, it's just that the MoD did not fund the detailed elements of the design process that would have allowed the ships to complete as CV-capable at an acceptable price. primarily a commercial / programme issue rather than technical.