Currently, the Update-Tools cmdlet enables users to kick off VMware Tools updates in their environment. However, the only flexibility is in not forcing a reboot and/or running asynchronously. When updating tools using the Flex/HTML5 interface, users are given the option for specifying Advanced Options within the Upgrade VMware Tools dialog.
Customers may have the need to remove a feature from VMware Tools, like FileIntrospection, and passing the appropriate configuration to the Advanced Options in the UI works. But, the same option does not exist for PowerCLI.