One of the things that's very, very difficult with individual certificates and LetsEncrypt's rate limits is to provide subdomains per-customer without leaking details (e.g. usernames) of other customers. If you don't want bob.example.com and alice.example.com on the same certificate, you can have a grand total of 20 users before you hit the rate limits.
This also affects systems like Sandstorm, which use randomly generated, unguessable subdomains per user session per "grain" (document), which may have (small) privacy concerns in some cases. Certificate Transparency would publicly publish every subdomain generated, even if the rate limits weren't a thing.