Simply put, nothing works.
If you do it by enrollment, Pinewood wins D5 every year. And privates that recruit -- and there are only a few -- punch way above their weight.
If you do it by recent history, the school that was good for three years thanks to a great class now is out of its league and will get pounded until an adjustment is made.
If you do it by this year's results, you wind up with brackets that favor the team that just missed going up a division and punish the team that is 16th out of 16, or eighth out of eight.
If you split the privates and publics, there aren't enough private schools to fill all the divisions, not to mention the fact that all the titles are even more watered down than before. Even if you just created three private divisions, there would still be issues as some bigger privates don't take sports seriously, and some small ones do.
In addition, the public school titles become even less impactful because no matter how good the public school, the fact that it didn't have to beat the privates in postseason can't be overcome.
So unless you have a solution, continual complaints about the CCS Open or NorCal seedings are pretty pointless. To me, the Open system is the best, though obviously far from perfect -- like the old line about democracy being a terrible way to run a country except for the fact it's better than any other way to run a country.