One of the features we are missing is a way to mark and edit trust settings on trust anchors, or root CA certificates. For example, a root CA may be trusted for SSL, S/MIME, or code signing. Browsers usually support this feature, as well as OS-specific keystores like keychain on OS X.
The work for this issue should also include enhancing the PKIX implementation to check the trust settings when validating chains. For example, a root that is only trusted for code signing should not be used to validate TLS certificates.