Plenty of money for fancy stations and never enough for the real meat of the system.
They are spending $3 Billion on new cars, plus $500 Million for the extension of PATH service to the Newark Airport Rail link station.
The Port Authority treats it's travelers better than the MTA, you don't want the MTA in charge of the PATH which is what you would have to do in order to make an integrated operation work. First of all fares would go up and service and quality would imediately go down, the MTA is in pretty bad shape as it is currently set up.
It's way better in the near and long run to have the Port Authority running the operation separetly as it is a good steward and provides sufficient funding and management, both are severly lacking at the MTA.
The NJARP proposal was very ambitious, it was never realistic because of the Political and Burecratic issues involved. Having the PATH's World Trade Center hub connected directly to the new Fulton Street Subway hub being built is a pretty good alternative.
The way to connect NJ to the Upper East Side is through NJ Transit, and eventualy a direct connection from NY Penn to Grand Central even though they have removed the plan from the ARC. Also extending the #7 train the West Side via the Farley Station would help.
Another idea worth perusing would be to extend the L train to 10th avenue then across the Hudson to Hoboken Terminal.