In order to make up the deficit of ~13,000 seats, SEPTA (and perhaps other agencies TBA) are laying on alternative services to try to avoid a complete rush hour meltdown. As of now, SEPTA has already extended rush hour service levels on the Market-Frankford and Broad Street Lines, the cancellation of the Subway-Surface Trolley Tunnel maintenance blitz, additional service on the Norristown High Speed Line and Media and Sharon Hill trolleys, and has additional buses on standby to augment service.
So what should the savvy commuter do in these circumstances?

1. Leave early, stay late, travel off-peak.
No matter what, peak capacity is going to be slammed. Everything is taking longer than normal to get from A to B. Take this into account, and also be aware that there will be both unexpected delays to published transit schedules, as well as extra transit service on little to no notice. Allow plenty of time for everything, and stay connected to service alerts. Off-peak trains seem to be running reasonably uncrowded, so if you can shift your travel plans, do so. I expect happy hours across Center City to be well-patronized.
2. Other transit services are your friend.
If you have the option of taking an alternate service into or out of Center City at peak hours in the peak direction, whether that’s Amtrak from Chester County, the NHSL from Norristown or the Main Line, a suburban trolley from Delaware County, or a CTD bus from large swathes of Northwest Philadelphia, Northeast Philadelphia and Cheltenham and Abington Townships, please do so. Not only will you make your own trip far more comfortable, but you will free up a seat (or one quarter of a square meter of standing room floor) for someone who may not have an alternative. We are all in this together, and we can only get through by working together. (Speaking of which, Amtrak needs to get it together as to whether or not it’s cross-honoring SEPTA passes on the Keystones. They should, but they also need to be consistent.) The least-crowded alternative service is the Broad Street Line from Fern Rock and Olney Transportation Centers.
3. Carpool, casually or otherwise.
SEPTA has opened up additional parking lots near the Sports Complex and has suspended parking fees at Frankford TC’s garage, and opened up additional parking in other locations, but a few hundred parking spaces isn’t going to do much in the face of a few thousand missing railroad seats. If you must drive in, please try to bring along a few other people from your area. Casual carpools, a/k/a “slug lines“, have yet to spring up in the absence of HOV restrictions on local highways, but are a good solution to the coordination problem of inadequate transit; if anyone hears of one setting up, or wants to start one, tell me and I will signal-boost it.
4. Lyft and Uber are still taxis. Use them accordingly.
Taking an e-hail taxi into the city is not a systemic solution to the crisis, although it might be the one-off solution to making an important appointment on-time when transit is running very late. Do consider them for bridging the gap to alternate services, especially in the suburbs, e.g. from Montgomery Avenue in Ardmore, to Ardmore Avenue Station on the NHSL, if the 103 bus isn’t practical; or from Malvern (where Amtrak doesn’t stop) to Paoli (where it does). Uber’s cross-promotion with SEPTA, offering 40% discounts on Uber rides to or from 11 selected Regional Rail parking lots, is still good even if you board a bus afterwards instead of a train.
5. Don’t take your frustration out on SEPTA.
SEPTA unquestionably did the right thing in taking the Silverliner Vs out of service. The defective part can fail catastrophically, causing a derailment, and nobody wants that to happen on a crowded train. Whether they did the right thing in buying them from Hyundai Rotem in the first place is a long story and controversial subject, but everybody involved in that decision has since retired, so the beleaguered conductor or customer service rep isn’t responsible (and isn’t in a position to fix it now). So take a deep breath, and save your anger for a worthier target.
Bicycle.