Well going via Philly you would be able to get a business class seat for your entire trip, whereas the Capitol Limited does not offer business class seating. On the other hand, the Capitol's seats are probably every bit as nice as the business class seating on the other trains.

The Capitol offers you the advantage of a really nice lounge to view the scenery, at least until darkness falls, and you food choices are much better since you have both a cafe car and a dining car. It also offers the advantage of a later departure from Baltimore.

The Philly route which includes the Pennsylvanian however does go around Horseshoe Curve, a very famous landmark. Additionally it has much better calling times in Pittsburgh, unlike the Capitol which arrives basically after midnight in both directions. And the Pennsy usually has a better on time record than the Capitol does. It however only has a cafe car, so your food selections are a bit more limited.