Although you can migrate to a Windows hosted version of vCenter, as of vSphere.NEXT (release as yet unknown) there will be no Windows version of vCenter so it is highly recommended that you migrate to the Appliance. Also the architecture of vCenter has changed significantly between vSphere 5 and 6.
Romain Serre wrote an excellent blog post on the process that can be found here
Step-by-step: Migrate Windows vCenter server to vCSA 6.5u1 -
Tom Howarth VCP / VCAP / vExpert
VMware Communities User Moderator
Blog: http://www.planetvm.net
Contributing author on VMware vSphere and Virtual Infrastructure Security: Securing ESX and the Virtual Environment
Contributing author on VCP VMware Certified Professional on VSphere 4 Study Guide: Exam VCP-410
