One problem I have with this tool is support for pre-computed public keys or CSRs. The client prefers to generate a new key pair for every certificate. Automated renewal that works the same way for existing CSRs as it does for regular certificates requires undocumented hacks.

Using the same key pair for multiple certificates is necessary for public key pinning, since Let's Encrypt only issues certificates that last 90 days. I would love to see this feature get developed further.