Since you cannot add a ESXi 3.5 to a vCenter 6, if you're using shared storage, the best approach will be present the volumes where your virtual machine is running to the new hosts, and then shutdown the virtual machine on the source ESXi 3.5 host, and on the new ESXi 6.0 host, browser the datastore, register the virtual machine in the inventory, power on the virtual machine and then migrate the virtual machine to a new datastore.
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Richardson Porto
Senior Infrastructure Specialist
LinkedIn: http://linkedin.com/in/richardsonporto