I've been fine tuning my own system for a few weeks now and wanted to share some knowledge with everyone that may or may not help.
What I found that helped most is adjusting the crop coefficient - in particular, adjusting this value to reflect ONLY the active watering months of the year. I live in Nebraska, so the default value (I assume for my zip code) is accurate for the year, but isn't realistic because my system is flushed and off for 6 months of the year at least. After I realized this and averaged in only the watering months coefficients, my flex schedules are keeping up pretty well.
In my front yard zones I've set the allowed depletion to 40%, which also results in slightly more frequent watering.
Finally, upgrading my personal weather station has been a big lifesaver. I went from an ambient ws-1090 to a davis vantage vue which is like night and day as far as reliability and accuracy go.
Now that things are dialed in, it's making it very easy to watch for and catch stressed parts of the lawn that prompt me to test run a zone for bad heads.
I do wish that when a hardwired rain sensor is being used, the system would be a little more lenient on rain skips. For instance...and i'm just pulling these numbers out of the air - if there's a 40% chance of rain, and the system would normally skip that watering due to this, that it would take into account the rain sensor and reduce the rain chance threshold a bit knowing that a hardwired sensor would catch active rain and stop watering.
That's a pretty minor quibble though.
Having used a CyberRain and Hydrawise until upgrading to the Rachio this year I can say without a doubt that it's light years ahead of those two competitors.