Pretty much anywhere, your best route is usually the interstate highway route. In Pennsylvania, this is especially true, as the secondary roads are usually mountainous so therefore have lots of curves that you have to slow down for. This kills your average speed.
Plus, the interstate highways are safer. The secondary roads can have intersections "whenever", and any one of them can have some yahoo run a stop sign.
But the deer don't even need an intersection to access the secondary roads, and have a much easier time getting close to the road before jumping out in front of you. On the interstates, the usually have to cross some open space before reaching the road, giving you somewhat of a chance to react and do something about them.
Plus, Pennsylvania seems to have some reason for making anything that isn't an interstate into a 45 mph speed limit road, not 55, so you really lose a lot of time if you obey that limit, or risk losing a lot of money if you don't.
It looks like the computer generated route is not that bad. The Pa. Turnpike is a scary road at times - try not to drive it in the rain or at night, and especially not when its raining and night. The edges have "Jersey barriers" that are inches from the edge of the road - real exciting when there's not so good visibility from trucks kicking up big sprays and limited traction from the water on the road.
Dave Head
