right (i think)... take NJ: the bus network has a bit more coverage than the trains, but the frequency of buses is very low and the routes are torturous, as a single bus wanders around various towns picking up people (a bus ride from camden to princeton -- approx 30 mins by car -- once took me close to 1 1/2 to 2 hours).
as for the trains: they are mostly geared to transporting people into NYC and back (for corporate benefit). take the two lines that cover the large swath of central, south and east jersey: the northeast corridor (shared with amtrak) that runs roughly from trenton to newark/nyc. and the jersey coast line, which runs from bay head (IIRC) to newark/nyc (if you want a train that goes further southeast, you are, AFAIK, SOL). both these lines have high frequency during the morning and evening commute hours, but not in a bidirectional sense, but in the direction of the work commute. at other times they fall back to a roughly once-per-hour schedule.
its also funny that these two lines, which cover more than 50% of jersey (i would think) interconnect only at rahway (a northeast town a couple of stations away from newark). so, if you wish to commute from the fairly densely populated monmouth or southern counties (which also are home to various corporations: lucent, prudential, among others) to any of the western parts (princeton, philadelphia, new brunswick, etc -- a heavily populated and corporate corridor), you first take a train all the way up to rahway and come back down the northeast line. but wait... it gets worse! remember, the schedules are loaded in one direction, so they will work against you in one part of your journey (going down from rahway if you are travelling in the morning, or going up to rahway if you are travelling in the evening).
as for the geography of NJ: the highest point is 2000 feet and it is northwest in the intersecting point of NJ, PA and NY states. a railroad connecting southeast and southwest NJ could run parallel to highways 33 or 195 (perhaps even taking advantage of land use rights and such).
--ravi