1) There is simply a hard cap on how many people you can fit on a six car train. The only way to expand capacity for the future may be to run more express/local trains in future years to balance demand, i.e. instead of two extra Elwyn trains making all stops, run the first express to Primos or Secane, and have the second be the local to serve the stops you skipped. I'm surprised this hasn't already been tried on the Doylestown or Paoli lines.
2) Under the circumstances, nobody cares about a 10 minute delay on these trains. It's still a far superior option to driving, either drunk or with all the other drivers who are drunk. Crowding, OTOH, is a serious issue.
3) As always, short-turning any train at Marcus Hook is... ill-advised.
4) One best practice SEPTA has lucked into is the long walk from the Parkway to Suburban Station, to attenuate the mass of the crowd. Stations right on top of a surge crowd generator, like the Meadowlands Station, seem to handle crowding very poorly.