Earlier quoted context omitted.
An interesting usecase of wildcard certs: when I do not want to publish the hostnames I am using. Sandstorm[1] uses unpredictable hostnames as one mitigation against various cross-origin attacks -- if the attacker doesn't know the domain of the app, he can't try to use XSRF against it[2]. [1] https://sandstorm.io [2] https://docs.sandstorm.io/en/latest/using/security-practices...
If you are willing to only accept SNI enabled clients (the vast majority nowadays), you can achieve the same by having one cert issued per subdomain, then configuring the web server/reverse proxy to use them. There are a few existing Nginx configs for that (search for "nginx dynamic ssl cert").
Anyway, Sandstorm developers told me that they wouldn't plan on using Let's Encrypt while it doesn't offer wildcards, so I think we are missing out on supporting this use case.