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yeah, it's called "shirley time" and septa isn't the only agency to do it. NJT and LIRR often have 10 minute cushions at either end of their runs. Not saying that it's OK but it doesn't make SEPTA special among commuter rail lines.
The article claimed only 6 lines use/share Amtrak lines. The R1, R2 Wilmington, R3 Media, R5 Paoli, R6 Cynwyd, R7 Trenton, and R8 Chestnut Hill are all subject to Amtrak dispatching. Since all trains, unless they're going to the yard, pass through center city and continue on to the suburbs on the opposite side they are all, at some point in a run, at the whim of Amtrak.
As far as some guy leaving Malvern at 2:30 to get to Suburban Station in time for a 6 o'clock class? The 4:27 train is supposed to get to Suburban at 5:23 - even if the train was a half-hour late, and these trains are more like 10 minutes late, he could still make it on time. But lets say this guy walks 10 blocks to class - there's another train at 3:55 that gets to Suburban at 4:50.
The bit about trains being held up at U. City is interesting. This is a high level, center island platform shared by the R1, R2, and R3. At rush hour trains pull in one after the other and immediately after leaving that station they have to go through switches and several signals, The R3 pulls off on to its own ROW after passing briefly through Amtrak territory but the R1 and R2 both have to merge with Amtrak traffic. Inbound the problem is much more severe - and the delays often in excess of 5 minutes because of the absence of a flyover (i used to ride the R2 to Chester everyday and the ride home was always delayed as we held for a northbound Acela so we could cross over their tracks to get to U. City)
It's also interesting because it points out SEPTA's big mistake in not going with high-level platforms for most of the system. At one point there were only 8 stations in the system, half of them owned by Amtrak, that had high level platforms. This made the center doors on the trains superfluous so they got rid of them and made the vestibule area an extra row of seats. Well now that there are more high level platforms it's still very awkward because everyone is still forced to squeeze out of narrow end doors that can only accomodate one rider at a time. Most people commuting are carrying something with them and people are always getting bags and boxes caught on the ubiquitous hand rails, points, and corners at then end of every car. U. City is also a station that sees a high percentage of reverse commuters so people boarding there also have to wait for riders to get off before they can begin boarding.
The new trains with center doors might solve some of this problem (but those are almost 2 years away) and a flyover just south of 30th St. for R1 and R2 trains will solve a lot of the problem.
As for lateness in general, again i'll say high level platforms for every station with ridership over 750(the center doors should make this much more efficient) center island platforms for stations that are shared with Amtrak (like Ardmore, Paoli, and Cornwell's Heights) so that Amtrak doesn't have to switch over to the local tracks to serve those stations . . . and get TVM's because even though most daily riders have passes, the people that don't take up enough of the conductor's time that it's difficult for them to make change and punch tickets and run back and forth to the doors at every stop - especially when you're in the middle of a crowded train with people standing in the aisles - as is the case on the R5, R3 and R7