One way is by counting the number of functional subsystems. For example algae do not have specialize reproductive organs while more complex plants do. Algae have fewer functional subsystems and are therefore less genetically complex. Does this need more explanation? I find it obvious.
You already made a false statement about humans having more subsystems.
My question, however, is not about complexity at the genetic level. How would you measure complexity of an unknown organism if all you had was the genome?