What many of you dont seem to realise is that ACARS outages are pretty common, even in the middle of Europe. ACARS comes in and out sometimes and pilots would think nothing of it, a station might be congested or doing some maintenance or whatever. Likewise transponders fail on occasion, not very often but again if a transponder failed during my flight I would think nothing of it, that is why we carry two of them. I would not know it has failed until ATC told me though and at that point i would just switch to the other transponder.
Flying is not like the high security prison some of you imagine it to be where a change in the FMC triggers loud sirens at a ground facility. There might be 101 reasons why I do or change things in my FMS. There are literary 100 of thousands of flights every day, 99.99999999% of them landing safely. The role of ATC is to make sure that in this very congested airspace airplanes do not collide with each other. They do not have a role to police what I input or not in my FMC.
Most serious emergencies would be dealt with by turning the aircraft towards a suitable landing airport, if heading out across the sea turning initially back towards the coast would seems sensible if confronted with fire or fumes. Although pilots have their own supply of oxygen there have been occasions in the past where the crew oxygen has been filled with nitrogen by mistake. If that was the case the crew would have been incapacitated quite quickly. Passenger oxygen has a limited supply of about 15 minutes, at altitude they would have been incapacitated too. Cabin crew do have portable bottles but can the fly the airplane? They can try and maybe they did but the portable supply doesn't last vey long at the flow needed if the airplane has depressurized, one way or another they would have ended up incapacitated too if they did not manage to descent the airplane to bellow 10,000 feet. Finally incapacitated people can do all sorts of funny things while trying to do something else, that is the nature of incapacitation.