In this case, I'd probably do a clean installation of all the components. First free up one of the hosts and disconnect/remove it from the current vCenter Server. Then upgrade it's firmware (if applicable), install and configure ESXi 5.1 and then setup vCenter Server 5.1 (unless you need Update Manager, you may consider the vCenter Server Appliance).
Once done disable HA/DRS on the old vCenter Server, disconnect/remove the hosts from it and add the host to the new vCenter Server. If the hosts have similar hardware, you should be able to vMotion the VMs and this way do a rolling reinstallation of the hosts.
André
PS: Regarding VMFS. Although it is possible to upgrade VMFS3 to VMFS5 on the fly (after all hosts are running the new version), I usually tend to create new datastores and migrate the VMs rather than to upgrading VMFS.