I would not be surprised if there were some major changes in the bus/rail emergency service plans as a result of today.
It's easier said than done. The problem you face is that it is so hard to plan for emergencies because there is no way of predicting what combination of service will be out of commission.
New Jersey Transit actually has some pretty decent emergency plans in place, but they involve the use of services like the PATH trains that were also out of service today.
Just think about what you had here today, and realize that there's no way in hell to accommodate all the people trying to get out of the city to the west. You had New Jersey Transit and PATH trains out of service, as well as the Port Authority Bus Terminal shut down with no power. They operated bus service from the PABT as well as possible, but they couldn't even accommodate a "normal" volume of buses because all of the passengers had to board the buses on the street instead of inside the terminal.
What made today even worse is that it occurred during the evening rush hour instead of in the morning. If it had occurred in the morning, then a substantial number of people would have simply turned around and gone back home. They didn't have that option today.