This month we started our upgrade journey from vSphere 6.0 -> 6.5 in production. We have had 6.5 running in lab for some time after the release last fall and we have enjoyed it so far.
As a part of this upgrade we plan to migrate to the vCenter appliance on both PSC’s and vCenter’s as this has gotten all functionality (i.e. Update Manager), and it scales to the same extent as the Windows one.
With the 6.5 release, even though it might not be an official VMware statement, I believe that the appliance is priority for VMware going forward and that the Windows version will eventually die (like the C#/Flash client story) so it seems that it would be wise to make the switch now.
Please be aware that if you upgrade your Windows vCenter 6.0 to Windows vCenter 6.5 you will not be able to migrate to a 6.5 appliance (https://kb.vmware.com/selfservice/microsites/search.do?language=en_US&cmd=displayKC&externalId=2147548).