There is a great session from Teched that address the issues with upgrading you’re private cloud. It can be watched at http://channel9.msdn.com/Events/TechEd/NorthAmerica/2013/MDC-B331#fbid=pJC3uNr4b0W
Basicly you want to do the upgrade in this order
1. Upgrade Systemcenter to 2012 R2. You need VMM support for the migration and SCOM and DPM for monitoring and backup. Use a separate database server for the VMM to make the migration easier
2. Evict one (ore more) fileservernode fom you’re file server cluster and create a new one-node file server cluster
3. Run the cluster migration tool to set up the new file server cluster with the same resources as the old one
4. shut down you’re VMs
5. Stop the filshareresource on the old file cluster
6. Stop the storage on the old file server cluster
7. Start the storage on the new file server cluster
8. Start the fileserverresource on the new fileserver cluster
9. Start you’re VMs
10. Break the old filserver cluster and add the nodes to the new file server cluster
11. Evict one (or more) node from you’re Hyper-V cluster and create a new Hyper-V cluster
12. Do a live migration of VMs to the new cluster so you can put another node in the old cluster in maintenancemode
13. Move another node to the new cluster
14. Do a live migration of VMs to the new cluster
15. Repeat untill all VMs and all Hyper-V nodes are moved to the new cluster
16. Upgrade the integrated components in the VMs
There is only one downtime in this process and it can be reduced by adding a new fileservercluster and new storage instead of reusing old hardware and by doing a storage migration in VMM to the new fileservercluster.
There is a risk by using one node clusters in the proccess because you are not high availability all and that risk an be redused by adding new hardware or by moving two nodes at the time and create new two-node clusters.
It doesn’t matter if you upgrade storage (file server cluster) first or if you upgrade the compute cluster (Hyper-V) first.