Yes, I agree - no matter how good the brakes are on the Gripen, it'll be a brave aviator who tries to set down on a pitching deck in the middle of the North Atlantic in complete darkness without a arrestor hook!
And yeah, STOBAR isn't as efficient as a catapult launch, either in deck space or in terms of aircraft payload. But, as the carriers were originally designed to have the ski jump, it would be the cheaper option to do, than re-engineering one of the carriers for these electromagnetic catapults that may or may not work, delaying the completion of the ships and forcing one to be mothballed.
Adding that wiretrap shouldn't cause too many problems as it's an established technology (unlike the EM catapults) which Thales, who are working with BAe on the ships, have past experience of. In addition, the design specified the ability for CATOBAR conversion at a later date, so the design architecture should be sorted - certainly they've incorporated the angled flight deck from the beginning, which makes things easier.
I'm not saying that in an this is the best solution, but it could be a way of making savings while also maintaining two deployable carriers. If the STOBAR changes could be done cheaply and quickly, and the aircraft we get to fly off them are both cheap and can be got into service this decade, then maybe, just maybe, we can convince the politicians to let us have both carriers after all! Later on we could always convert the carriers to CATOBAR and buy more expensive planes when we have the money, but in the meantime the Gripen/STOBAR configuration could work as a cost-effective interim.
On the question of stationing aircraft in theatre, it makes sense if we plan to be there a long time, like Afghanistan, rather than maintaining a carrier in the gulf year in year out to provide air support. Hopefully, the Gripen's short take off ability would mean not so much concrete to be humped through the Khyber Pass...It's also recommended to give the RAF FJ pilots a job to do that makes them feel wanted, or else they may start tinkering with the maps again and shifting Australia 300 miles north west again!
And yes, here's to a Christmas spent theorising what to do if you were in charge of the MoD! Personally, I'd rather cut the High Speed Rail link between London and Birmingham and buy two more carriers and money to spare! I mean, who needs to get to work 30 mins earlier when we can have 21st Century gunboat diplomacy!