Idea:

MetrO is an awesome app for finding out what train stops where, but its geared for rapid transit where headways are short enough that there isn't really a need for a timetable. For commuter rail, the schedule becomes a lot more important. MetrO + timetables would be much more helpful here.

Extra special features would be to generate a schedule showing you all the different ways to get from src to dst (e.g. NYC -> NWK (NJT|PATH) -> TRE (NJT) -> {CAM (NJT) -> PHL (PATCO)|PHL (SEPTA)}.