Afaik there is no cmdlet available in the current release that allows you to do such a thing.
In fact the VirtualMachineRelocateSpec object, which controls the CloneVM_Task method, only foresees a datastore for the new VM.
That is the SDK API that is used internally by the New-VM cmdlet for cloning a VM from a template.
The only way I can think of to do this would be something like this
- create/clone the new VM
- unregister the new VM
- set up a datastore provider to the datastore where the new VM is located
- create, in the datastore provider, the new folder structure
- move all the files that constitute the VM from the original folder to the new folder
- register the VM with the VMX file from the new folder
But I'm not sure if nesting folders like that on a datastore is a "best practice".
I would go for dedicated folders under the VM and Templates view in the vCenter.
Then you would still have the folder organisation, not on the datastore but in the vCenter.