As I see it, automation is NOT LE’s main aim.
LE’s main aim is widespread adoption of TLS.
Automation is a means to an end - to make it as easy as possible so that admins will actually bother setting up TLS.
Forcing short certificate lifetimes actively gets in the way of our main aim, in the name of encouraging automation.
Finally, there is a fundamental difference between encouraging short lifetimes and imposing them.
By all means, make 90 days the default. But give users the choice, by allowing longer options too.
This is why some people are angry - because you are taking the choice out of the hands of the user. To assume you know better than the user is perceived as arrogant and controlling.
I know you are doing that for the right reasons (because you think it’s better security practice) but it will be counterproductive in the long run, since it will act as yet another barrier to adoption of TLS.
There are plenty of use cases in which short lifetimes are not appropriate (no need for me to repeat them).
I will just add one more - general prevalence of short certificates creates extra work for anyone that is pinning/paying attention to what certs are being served to them. There are good reasons to do this, since the CA trust model is really problematic.
Use of a consistent subject public key over longer periods does mitigate this issue, but encouraging a culture of short-term certs needs to go hand-in-hand with vocally encouraging a culture of long-term keys. Anything else is irresponsible in the context of widespread surveillance and well-funded MITM systems.
Anyway, that’s it. Hope you are able to listen to what people are saying and change your mind.