Reference: http://blogs.technet.com/b/askpfeplat/archive/2013/04/22/choosing-a-hash-and-encryption-algorithm-for-a-new-pki.aspx

” If you absolutely must support legacy applications that don’t understand CNG algorithms, and are building out a new public key infrastructure, my advice today is to build two hierarchies. The first hierarchy – a legacy hierarchy if you will – would have a lower key lifetime aimed at a documented point at which legacy applications and devices MUST support CNG algorithms. You could issue certificates based on this “lower assurance” hierarchy for a limited time only to legacy clients, perhaps with limited EKUs and a specific Certificate Policy attached to it. The second PKI would be erected with more current algorithms and key lengths to support more current clients and with much longer expiry periods. When building that PKI, you could follow the stronger guidance put forth in the Federal CP and choose SHA-256, or SHA-384 along with RSA Keys of 4096 bits or ECC keys of 256 or 384 bits. I agree that this adds complexity, but I find in the IT industry that we’re constantly dragging older applications and devices into a new security world – often, kicking and screaming the entire way.”