I'm not an expert, especially on the regulatory framework, but I can make a limited answer.
In some ways aircraft already are making incremental steps towards more automation and fail-proofing:
Airplanes already try to revert to basic functionality when something fails. Localizer beacon failure doesn't disengage the whole autopilot, and many autothrottles can work with one engine out. There may be some room for improvement in specific areas though - but bear in mind many of these sets of redundant sensors are already designed to have less than one complete failure per million flight hours.
Some of the problems don't lend themselves to an easy solution- if you're engaged in altitude hold and you lose your air data sensors, how do you measure altitude to maintain altitude? You could create a new sub-mode for level flight based only on the IRS, but this would be a lot of complexity compared to the alternative of hand-flying or just going to a basic pitch hold mode.
Sure, you could get around these dangerous scenarios by taking more authority in and reverting better to basic systems or modes when something fails, for example going into speed on pitch when both engines fail. Or in the case of Indonesia flight 8501 that you mentioned, forcing a backup flight computer to always be on during flight and somehow refusing to allow a dangerous roll to occur at the moment the autopilot disengages. However, in all these situations, you're trying outsmart the pilots and take decisions from them, which is... complex.
Some manufacturers give the pilot full authority, some limit the pilot only to what's known to be safe. While in my experience avionics engineers are happy to overthink things and try to idiot-proof their systems, these kinds of new systems come with a lot of difficulty in human factors testing, increased complexity, etc. and so changes are only made incrementally.
There is some regulatory work I'm aware of behind this. For example, planes are designed to be predictable and deterministic: the thought of untested scenarios or non-deterministic code keeps certification authorities up late at night. This limits development to maintainable, modular segments of flight and behavior. It's also easier to certify and train for incremental changes than a complete redesign, especially given how incredibly complex modern avionics are.