Cloning the disks to different Datastores can be accomplished using vmkfstools -i . Cloning this way only clones the .vmdk files and doesnt give you the ability to customize, you would need to manually create the VM and attach all the disks, which for some is more work then its worth.
Other then doing it this way I'm not sure you can do what you are trying to accomplish.
When you run your clone operation, when you are asked to select the destination datastore, don't you have an Advanced button? If you click on it, you should have access to a menu where you can choose a different destination for every virtual disk.