Terrific write-up. I'm glad you're enjoying many of the new features in SAM 6.0. Regarding your SQL servers being perpetually in a critical state, this is a known issue that we are currently investigating. We should however have this nailed down before we reach release candidate.
To your question of baselining, we couldn't agree more. That's why we added this feature into SAM 6.0. You likely haven't noticed it yet as it's buried pretty deep. If you go to any application you have assigned (AppInsight of template based), edit the application and expand one of the component monitors and override the thresholds from the template you will be presented with two options. The first is pretty straightforward. Click the "Use Latest Baseline Thresholds" will calculate warning and critical thresholds based on the last 7 days of polled data.
The second option "Latest Baseline Details" opens up a new Window that shows the full details of the data those recommended threshold calculations were based upon. This allows you to have a better understanding of the data, and gives you the ability to make informed decisions on what those thresholds should be defined for your environment.
