Plan all the involved steps accordingly, evaluating the impact of new features and the improvements that can be applied to the current environment. An upgrade order of the virtual components should be established to avoid potential problems. For example, the vSphere platform requires first upgrading the vCenter Server then the ESXi hosts to avoid communication issues within vSphere components.
If you need to consolidate an SSO domain, this can be done only on vSphere 5.5 and involves a change of architecture since you need to deploy the PSC from embedded to external. Check out the VMware KB 2033620—How to repoint and re-register vCenter Server 5.1 / 5.5 and components at https://kb.vmware.com/kb/2033620 for SSO consolidation. PSCs are the first components to upgrade, then go ahead with vCenter Servers. If you migrate from vSphere 5.5, before starting the upgrade procedure, you need to break Linked Mode if configured in your network.
Since VMware has deprecated the Windows-based version of vCenter Server, it's worth migrating directly to the Linux-based vCSA, taking advantage of the new features introduced in version 6.5, such as embedded VUM, VCHA, built-in file-based backup restore, available in the vCSA only. If you have vCenter Servers with external PSCs, get both components on the same version to take advantage of new features. vSphere 6.5 provides a Migration Tool in the installation media that supports migration from vSphere 5.5 and 6.0 environments.
The vCSA installation can also be performed through script using CLI commands that allows the automation of the installation procedure, making the process faster:
When PSCs and vCenter Servers have been upgraded, you can start migrating ESXi hosts. Although ESXi 5.5 is supported in version 6.5, new vSphere features won't be enabled until hosts are upgraded as well. vSphere 6.5 introduces VMFS 6 as a storage filesystem that brings a lot of improvements, such as Automatic Space Reclamation (ASR) and the support for 4K Native Drives in 512e mode, enhancing the core storage space performance.
The vSphere Storage vMotion feature can be used to move VM to other datastores while you upgrade the existing datastore to VMFS 6. To identify the VMFS version used in your datastores, in addition to vSphere Client (select the vCSA object and go to the Datastores tab), you can use esxcli commands from the ESXi command line:
esxcli storage filesystem list
The same information can be retrieved using PowerCLI:
Get-Datastore | ft Name, Type, FileSystemVersion
If you come from a vSphere 5.x environment, licenses must be upgraded to version 6. Keep in mind that if you have a 60-day, fully working trial when you install vSphere then your environment will continue working while you upgrade the licenses.
For large environments, you could schedule the upgrade in different maintenance windows by upgrading the vSphere environment in stages. You can start by upgrading all PSCs, followed by the vCenter Servers, then the ESXi hosts. Planning the upgrade process in different steps, reduces the maintenance of the environment in three shorter time frames limiting the downtime. To avoid issues, upgrade each vCenter Single Sign-On or PSC one at a time.