I agree this is an issue. I'm out of PHL and I frequently will compare EWR-SFO with PHL-SFO. EWR-SFO is often nearly half the price as PHL-SFO. EWR-SFO has better frequency but it is inconvenient to drive up to EWR. Ironically, on PHL-SFO, I have a higher chance of upgrading even on an A319 than on EWR-SFO where I have nearly zero chance. If I actually had some chance of getting upgraded, I'd probably fly EWR-SFO more often.