Also, if you own a very big amount of subdomains (say > 100), you want to minimize the number of certificates you want to manage/renew for easier maintenance and renewal.
I don't agree on this one. The whole point of the ACME protocol is that it allows for automated certificate management. Thus, it shouldn't matter if you manage 1 of 10000 subdomains, because you should automate it anyway.
Also, if for some reason the automated process fails, I'd rather have one subdomain go down, than all of them.
Also, if for some reason the automated process fails, I'd rather have one subdomain go down, than all of them.