What I have gathered from other threads on the topic is the way the 12V battery is used in a Model S is atypical. In ICEs, the battery is used to start the car, the the alternator takes over. In the MS the 12V battery runs everything not related to the drivetrain all the time--this duty cycle is very different from the intent of the battery's designers, hence the failure rate.
That's not a valid comparison. In fact, the situation when driving is much like an ICE - the Model S DC/DC converter supplies the 12V loads and charges the battery, just like the alternator in an ICE. In neither case is the battery disconnected once the DC/DC or alternator gets going.
The major differences between Model S and ICEs are the amount of power used while the car is 'switched off' (higher on the Model S), and the size of the battery (smaller). The combination means that the battery gets cycled while the car is parked, with the DC/DC powered up occasionally to recharge it.
You might say "why doesn't the DC/DC run all the time to save cycling the battery", but I imagine the answer is that the power taken to run the contactors, main pack battery management etc. would be just too large.
My theory is that whoever specified the 12V subsystem on Model S expected the software guys to do much better on power save in the various on-board computer systems, but with the rush to get the car out of the door that was never achieved, leaving the power drain much higher than it should/could be, and making what was originally a reasonable choice of 12V battery turn out inadequate.
It's always much harder to put power management into a system after it's been built rather than doing it from the beginning, so it's not clear whether they have simply never had the development time to get it right, or if some architectural mistake was made early on that makes it impossible to fix now.
It's also not clear to what extent the 12V system is "still broken". Every time we hear of 12V problems, people cry "why is it still not fixed", when many times it's not the 12V battery that was the root of the problem - almost any problem in the high voltage system will cause that to shut down, and then within a few hours the 12V will go flat. So the low 12V warning may be the first thing the driver sees when it wasn't a 12V fault at all.
Undoubtedly the 12V would last longer if it was cycled less, but the current life is probably tolerable if not as good as we'd like.