The most important was clearly obtaining the PLC zero days to infect the physical machines. It's unclear to me why you choose to be so explicitly obtuse but in any case, for your own personal edification, feel free to read some details on how it went down -
[0] https://www.wikiwand.com/en/Stuxnet
[1] https://www.wired.com/2014/11/countdown-to-zero-day-stuxnet/
We’ve found instead that the NSA can just take over your unpatched computer easily instead of putting in the effort of hacking Let’s Encrypt.
Please explain your comment about how key signing ceremonies stop people from being bribed. The creation of those keys creates a root of trust but doesn't stop leaf certs from being generated.
Still, there are hundreds of publicly trusted CAs so the chance for exploitation is higher.
On the other hand individual security professionals might have wildly different ideas about risk tolerance and convenience, which they also have privilege to change on the whim.