When a user without a certificate logs on the first time to an ASA remote access VPN that has a connection profile requiring certificate authentication they will have to request one via AnyConnect (if the ASA is setup with its own CA) or via a SCEP portal (another option).
If a certificate had been pre-deployed or otherwise is already in place, you have a number of options on the ASA to do things like pull certain fields from the certificate to assign users to different connection profiles, pre-fill the username (and even the password), check for certificate revocation, etc.
One common use in the US government is to require use of certificates stored electronically on an ID card and inserted on a card reader on the PC. Only when this certificate is found is the user allowed to authenticate using their username and password (which is from the AD authentication source). Thus the certificate is used as part of a two-factor scheme. Of course if you already have token-based two-factor authentication, this use case might not be attractive to you.
