That is the biggest challenge...What to do with A League type teams that finish 4-6 or 5-5...I think a larger B/C only bracket of 16 teams would be ideal, a 16 team A league bracket, and then an 8 team bracket with those schools that are playing a different sport than the rest of us. Less brackets would allow for putting similar schools together into one bracket, rather than spread out over four different brackets. This is how the NCAA does it for all sports, and I think could be a decent guide.
The last I checked, for basketball, it's pretty common for "mid-major" conferences such as Ivy or Big South tend to get only 1 team into the NCAA tournament, while the ACC, Big 10, or SEC get 6-8.
SSLG also has a good question...At this point in time, there appears to be little to no purpose to the CCS playoffs, other than just extra games. They do not determine much other than determining the best team in a group of 8 schools. The baseball structure is even more puzzling, with 48 teams spread out over 6 divisions.
Divisions are meant to be structured as competitive levels. D-I is supposed to be superior to D-II, which is superior to D-III, etc. Not all sections view it this way as the top team in the SJS has occasionally come from D-II. The division winner is the top team in that competitive bracket, then gets to go on to compete at the state level in a similar competitive bracket.
Even in other styles of playoffs, the idea is always to have a level playing field, but those often fall very short.
In the SS, they had league-based divisions for a very long time. Well, that meant that teams in leagues that were put together more for geography or because they were simply from the same school district were forced in D-1. They're decent at baseball, so they should also be good for football, yeah? Long Beach Wilson was average even for the Moore League... so great! Let's make them play Mater Dei in the playoffs! That's fair, right?
In the NCS, enrollment is the main determination. Ok, then you've got Cardinal Newman and Marin Catholic beating the crap out of the small public schools pretty much every year in D-IV. That's fair, right?
There is not going to be a perfect system for everyone. Someone is always going to have to be an 8 seed somewhere in the CCS, but we don't entirely know that this domination from Serra is going to become another DLS situation. Everyone forgets that just two seasons ago, 8-seed Aptos was tied with #1 St. Francis after 3 quarters in their first-round game in D-I.
Every year, though, the crying we get is really about one program: Carmel. The "other" Padres feast on lower-level teams all season long, then their fans (and local sports writers) whine about not getting to do the same in the playoffs. Well, I'm sorry... a section of 94 teams isn't going to alter its structure just for one program. If they end up as the #1 seed in D-III, great! If they get moved up to D-II as the 8-seed? Them's the breaks. Next year, my alma mater Salinas will almost certainly be playing in D-I against the WCAL powerhouse teams, but you're not going to hear me crying about it. It's just how it goes in the CCS.