The flattest route across PA is probably the northern tier, which is traversed by PA Bike Route Y:
ftp://ftp.dot.state.pa.us/public/pdf...state_mapY.pdf
However, my understanding is that at least some of that route has been polluted with truck traffic from fracking activity. Also, it doesn't start near Philly.
Anything across the center of the state is likely going to be harder than Route S.
Some of what might be contributing to the altitude numbers for Route S is that, heading west, it does not join the GAP until Rockwood and then leaves it at West Newton. I beleive the section of Route S between Bedford and Rockwood through Somerset is tough. This section parallels the Allegheny Tunnel of the PA Turnpike, so it's likely crossing the Allegheny Mountains there:
ftp://ftp.dot.state.pa.us/public/pdf.../Bike_S_11.PDF
If you were to get off Route S in Bedford and take U.S. 220 to Cumberland to pick up the GAP you would miss that stretch. U.S. 220 south from Bedford has a lot of ups and downs, but nothing that looked like it would be too bad going the other direction. And you can save yourself a lot of grief by hanging a right off U.S. 220 onto SR 807/Bedford Rd. NE before you get to Cumberland. Take that straight onto Bedford St., which will take you into the middle of town. Doing cuts out some giant rollers on U.S. 220 between SR 807 and Bedford St.