I think probably the biggest hurdle in having either SEPTA or NJT cars in a museum is that they are seen as "too new", and not "historical" enough.
I think the major problem is that most of these commuter agencies are considered to be "antiseptic", if that makes sense. They have no history, no legend. Even though its equipment and routes originated from those legendary railroads like the PRR, Reading, CNJ and Erie Lackawanna, they did not inherit that legend. In the eyes of the people doing the railroad preservation, the legend died when they were merged into oblivion, and "soulless" government owned companies took over.
I suspect people clung to the GG1 not just because it was a great locomotive, but because it was undeniably PRR no matter what coat of paint you slapped onto it. It was symbolic. If the PRR didn't have the legend it did, the GG1 would just be another vague electric locomotive.
I think this is readily reflected in existing museum collections. To be sure, plenty of former SEPTA and NJ Transit pieces are in museums, but many have specifically been repainted out of their former schemes. The URHS is good example. A large part (maybe even a majority) of their equipment belonged to NJ Transit at some point. However, NONE of them retain NJ Transit markings apart from a heavily vandalized E60 Which I've heard rumors will also be loosing its NJ Transit paint in favor of the Amtrak Phase II stripes it was delivered in. Two locomotives have the NJ DOT blue-bird scheme, but are technically not NJT. Their one NJ Transit E8, they repainted into a completely obscure New York Central experimental scheme, thinking that was more worthy of preservation than its ACTUAL paint scheme. Similarly, the passenger cars aren't painted up for NJT. The URHS has a fleet of Jersey Builders but painted them up in some really bland grey paint.
SEPTA is in an even worse position. First of all, there is very little "SEPTA" equipment retired and available for museums. The diesel stuff retired in the 1980s has all moved on and either been rebuilt, scrapped, or restored to prior owners. I doubt strongly you'd ever be able to convince the owners of the surviving FP7s to paint them up in the SEPTA paint. There are a handful of rotting SEPTA MP54s out there (or did those finally disappear?) and some Reading cars still in SEPTA paint, but I doubt the owners are interested in preserving them that way, given the popularity of the "blueliner". Clearly, no one was interested in the Silverliner II/IIIs. The one SLII set aside is apparently without a clear owner, because I keep hearing different stories about who it belongs to. As far as I can tell, no one is seriously considering (AKA, has the money for) saving that Silverliner III. The Silverliner IVs and Vs are not going anywhere in the near future. There wasn't a whole lot of interest when Amtrak retired its AEM7s and so I doubt the SEPTA AEM7s/ALP44s are going to be popular preservation choices either.
Now to be clear, I don't necessarily agree with the sentiments I outlined above. I think these commuter trains have been the point of contact that most of the public has had with trains for the past 40 years. They may not have corporate legends behind them, but they've been out doing all the same jobs (even more so!) and probably deserve to be remembered.
However, convincing someone in a preservation group that a Silverliner IV will have as much value as some ex PRR diesel that the average person has never encountered, will always be a hard sell.
Elite Juice Jack Modeler.