I actually rather hate the setup SEPTA currently uses for producing its schedules online. It looks really unprofessional compared with what other transit agencies do (but of course, so does the whole website). When I'm in Pittsburgh, my secondary residence, and make use of their system, I rather like the fact that their schedules are presented in both HTML and PDF.
Now, perhaps it's that I have a good connection and can download them quickly, but I prefer the PDF over HTML. The Port Authority's (here in Pittsburgh) schedules are legible when shrunk down to letter size. Having never used SEPTA paper schedules, I'm not sure that that would be the case, but I can say that there are designs for paper schedules that print well off the PDF.
If the file is made well, it really shouldn't be any harder to find the information than on the paper schedule on which it is based. And if its made really well and you have a good viewer (I don't use the usual acrobat) you get some nice layer features and regardless of viewer "find" (ctrl-F or cmd-F) should work.
-asg