Yes, EWR and JFK are in many ways separate markets, even though they both serve NYC. I think you are right on the money about competition. UA and CO were the only airlines to offer non-stop SFO-EWR flights and now that they are merging there is just one carrier serving that nonstop. JFK-SFO on the other hand has AA, DL, B9, VX, and UA (did I forget any?), so it is often far more price friendly. To answer the OP's question, I don't think next year will be any different.

Ironically, I find the UA ps SFO-JFK flights to be far more comfortable than the CO or UA EWR flights. The premium seats offer much more room and wifi is a great amenity, although the CO food trumps even the UA ps food.