NJ-1 would run down the median of Route 42 and the Atlantic City Expressway to Williamstown. NJ-2 would run down the median of Route 55 to Glassboro. Both of these alignments may or may not relieve congestion along these highways, but they would almost certainly have another, less desirable impact -- increasing pressure to convert open space and fertile farmland into sprawling development, much of it in environmentally sensitive areas.
Only NJ-3, which would run along an established rail line through the center of several historic Gloucester County towns, along the Conrail right-of-way, would be a win-win for the region and its residents. Not only would this routing relieve traffic congestion on area highways, but it would promote the revitalization of these historic centers by encouraging walkable, mixed-use development around the stations.
It's generally a bad idea to run train lines down highway median strips as it doesn't do much to change land use patterns.