I'm not saying that every part shouldn't be accounted for, or that new rules should be passed right away without a detailed evaluation. But if the FAA had a single integrated system for airlines, manufacturers and inspectors this bolt issue would be over a lot faster. They could send out a personalized alert to everyone recorded as operating an old 787, wait for them to upload the ultrasonic data, run the analysis and give immediate feedback if something needs to be replaced.
Even Boeing could flag the issue a lot faster if they had a good analytics pipeline looking for correlations between fatigue rates and different aspects of production. That would mean taking inspection results from all their customers, and only the FAA can help with that.
You misunderstand the root of the issue: a single failure can lead to the deaths of hundreds of people and massive political blowback. Automation is great! Deploying automation always comes with headaches, and here the headaches would be unacceptable because they could easily lead to hundreds of people dying. Jetliners all already have fully digital datalinks, but clearances are still given over analog radio; pilots have the authority to decline a clearance whenever they feel it necessary. How would automation handle that?
The same administration software would have to work across the entire world, including in countries with different aviation systems and standards. Lots of airlines send jets for maintenance in different countries; they would need to trust this system over paper records.
FYI - the FAA is testing out ATC automation for general aviation, which is much more accident prone and therefore a better candidate than commercial aviation which has a sterling safety record. I think if it works there we might see it in commercial traffic, but it's a long road to get that many 9s.
These airplanes are flying all over the world, the inspections need ultrasonic data, and the FAA has to validate that all of them are done. Even identifying this issue required lots of bureaucracy.
Multiply that by the number of airplanes and airplane models and it's easy to see why they move so slowly: when you are putting millions of people in the air each day, enforcing absurdly specific rules with an iron fist requires a monster of a bureaucracy.