I was moving a customer from vSphere 4.1 to 5.1. I have read that it's best to create a new datastore with VMFS 5 and migrate VMs over. The new hosts could see both new and old datastores.
I initiated a Storage vMotion to move a VM from the VMFS 3 to VMFS 5 datastore but it was taking ages. The performance charts where shows approx 17 MB/s. I rechecked my configuration and all was good. I decided to move a VM from a VMFS 5 datastore to another VMFS 5 datastore and this time the throughput was over 117 MB/s
Turns out that because the VMFS3 datastores have a 2MB block size and the VMFS 5 datastores are automatically created with a 1MB block size this slows things right down.
So allow plenty of time and be patient when migrating from VMFS 3 datastores :)