This is exactly what I said would happen if win%'s point gain was overly buffed back when people were complaining because 'popularity is too powerful'. Of course back then the win% difference was much smaller because there wasn't such a skill split, so popularity made a larger difference. I predicted, correctly so, that the skill difference would grow over time and the point divisions at that time wouldn't be such a problem in the future and would balance themselves out, maybe with minor tweaks at most. But people kept complaining and changes were made, and now popularity is so underscored in comparison that, combined with the skill split, it basically means nothing.
Now people are mad because popularity essentially makes no difference with how things go down, so all the good players end up on one side by figuring out where most of the kids will go, and crush the new people in an event that isn't even supposed to be competitive (that's what tournaments and squadding are for) but instead is for fun.
What did you expect? This is what many of you asked for back when splatfests were new. Enjoy your predictable results and your overabundance of sea snails.