certonly can interact with a human user (for example, with --manual where user action is required, or to ask questions about options that weren't specified on the command line); renew can't
renew can renew many certificates in a single run; certonly will only generate at most one new certificate per run
Normally, we expect that systems will run certbot renew twice per day automatically, in order to renew all certificates that are getting close to expiry. However, the ability of certbot certonly to renew individual certificates upon request is intentional, in case users have a need to do that.