I always fly out of Philly.... we have never had any issues at all... our flight has always pulled out early. We do fly AJ though and they have a very early AM flight... as far as the baggage is concerned never had it lost or took a very long time to get the luggage... you can't compare a small airport to a very large one and like other people have pointed out it is in a very congested area with air traffic.
We always fly A/J out of Piladelphia. We have never had a problem. We flew back to PHL last month and there were more customes officers at 9:30PM that there were passengers. They were directing us to open check points. It took us about 25 Min's from the time were off the flight till we were through custome and on our way home.
Granted it depends what time your flight lands but we have never had a problem except when US Air lost our bags!