The stations are indeed close together--they date from a period in the 19th century when the (now) inner suburbs were already being developed and people walked to and from the station, so many of them are about a mile apart. This means that acceleration and braking are more important than top speed, which favors EMUs. There is also frequent congestion close to the Center City stations; e.g., northbound at 30th St., 6 double-track routes (not counting Cynwyd) converge to 6 main tracks, which narrow to 4 from there through Center City to 16th St. Jct., where Norristown branches off, after which other lines gradually diverge. It would take Swiss precision, which is not part of the culture here, to fold in all the incoming trains while not getting in each other's way. Also, all junctions north of Center City are flat, which doesn't make it any easier. As if that weren't enough, there are posts in the Philadelphia forum indicating that PTC, with cab signals only except at interlockings, has simply dumbed things down to the point that overall speeds are reduced. I should also mention that three of the lines (Thorndale, Trenton, and Wilmington-Newark) are dispatched by Amtrak, as is Chestnut Hill West for a short distance, so there are plenty of obstacles to timekeeping.