The best I've found so far is Alex's Brown Bag in the Banker's Hill area. At first I thought my co-worker (who is from Philadelphia) was putting me on since the place looks like such a hole in the wall and I became even more dubious when he told me authentic Philly Cheesesteak comes with cheese wizz instead of melted swiss cheese but I decided to give it a try. To my surprise it was actually damn good and cheap! I also tried a bit of Scrapple which is supposedly another culinary tradition from Philly though I was less impressed with that.
So now I'd like to compare so I'm on the hunt for the best Philly Cheesesteak in San Diego. Does anyone have any suggestions?