I had a lot of questions on this recently.
I was told that Sites take up the most memory on the console and you should have as few as possible.
I have a discovery Site, then a Site for each of the credentials I have with Schedules for each Engine Pool.
Tagging and Asset Groups are a good way to carve up your data.
I use to use Asset Groups for tagging, but too many Asset Groups is a performance issue as well.
I now Group where I want to Report and Filter, and Tag for enrichment.
There is a balance between access, resources, and management that all need to be considered when laying out your data.
See this thread: New Site vs. Targeted Schedule?