I have a Hyper-V threshold file in PAL to analyze the host machine because you need to look at the "\Hyper-V Hypervisor Logical Processor(*)\% Total Run Time" to see what the physical processor are doing. Task Manager on the host and % Processor
Time are only measuring the Root Partition. Think of the host operating system as another virtual machine that happens to be special.
Yes, virtual machines tend to have high processor queue lengths with low CPU utilization. This is known and is not an indicator of a problem. It is the way the that counter is collected that makes it inaccurate.
Anything that uses a percentage like % Processor Time will be slightly skewed on virtual machines, but typically it's within 10 to 20% deviation.
Other than that, I analyze virtual machines just like any other.