You can replace the VMCA root certificate with a third-party CA-signed certificate that includes VMCA in the certificate chain. Going forward, all certificates that VMCA generates include the full chain. You can replace existing certificates with newly generated certificates.
If you use VMCA as an intermediate CA, or use custom certificates, you might encounter significant complexity and the potential for a negative impact to your security, and an unnecessary increase in your operational risk. For more information about managing certificates within a vSphere environment, see the blog post titled New Product Walkthrough - Hybrid vSphere SSL Certificate Replacement at http://vmware.com/go/hybridvmca.