Comparison between VMFS3 & VMFS5
- You will use VMFS3 if you have a vSphere environment which is mix of vSphere 4.x (also 3.x) & 5.x hosts. Presently VMFS5 datastores cannot be accessible to hosts running an ESXi version less than vSphere 5.0
- You can upgrade from VMFS3 to VMFS5 but cannot downgrade.
- On upgrading a VMFS3 datastore, the datastore starts to use GPT partition format only after the datastore has been extended (within the extent) beyond 2TB (less 512bytes). Not sure if the behaviour is similar for a spanned volume as well, but I believe that is how it should behave.
- Storage vMotion (migration across datastores) between a VMFS3 and VMFS5 volume is supported if you are using a vSphere 5.x host.
- vMotion (migration across hosts) in vSphere 5.x is supported in either cases when shared storage is VMFS3 or VMFS5.
For additional information refer vSphere 5.0 configuration maximums guide.
I would also suggest to go through the VMFS5 FAQ document which has some great information.