The top of the the ECNL teams are the best, without a doubt, but in So Cal that difference is much more dramatic than it is nationally. But if you look at Surf Cup only, there is often just 1, and maybe 2 GA teams in a bracket with 16 teams. Even if all teams were exactly equal, you'd only expect very few GA teams to end up in the finals.
It would be wonderful to see the top GA teams (Colorado Rush, Houston Dash, Michigan Nationals and the like) playing the top ECNL teams more often, but the different platforms like to keep them separate, it seems.
To be sure, you'd have to see whether the top GA teams were signed up for Surf Cup - if you've got the time to check. But until GA strengthens its ranks in the Southwest, there's not much argument ECNL has the stronger teams at the top of the standings for sure.
Once you get to the middle and bottom of the ECNL teams, it's less clear, though MANY people have STRONG opinions on it!