It basically depends on your needs whether to use the vCenter Appliance or the Windows version. The Appliance has some limitations (see e.g. VMware KB: Services bundled with vCenter Server Appliance ) and if you want to use Update Manger, you need to install it on a separate system. The appliance is also limited to 5 hosts/50VMs (like vCenter Server for Windows with SQL Express).
On the other side - if the limitations are not important for you - the appliance is way easier to install and to maintain.
Regarding your initial question about HA. Although vCenter Server is used to configure HA, it's not involved in HA functionality. Once configured HA is handled by the hosts only.
André