While the Port Authority’s future has been in question lately, the bi-state agency’s present has come under the microscope as well Though we’ve long known just how the Port Authority has become a victim of its two overseers and how its projects have strayed far from its core mission into the realm of political whims, a new report issued by NYU Wagner’s Rudin Center for Transportation Policy & Management underscores just how deep these problems run.

The report, authored by Mitchell Moss and Hugh O’Neill, is available online, and Matt Flegenheimer of The Times offered up a succinct summary of the key takeaways:

The report…says the agency spent more than $800 million from 2002 to 2012 on “regional projects” chosen by the governors’ offices. In the coming years, the pace of spending on zero-return state projects is expected to accelerate. As a result, the most powerful testaments to the agency’s peril, according to former agency officials and transportation experts, are not found amid the bridge access lanes of Fort Lee, N.J.

They can be traced to the grounds of industrial parks built in the Bronx and in Yonkers, with little obvious transportation purpose, or along the Pulaski Skyway, which the agency agreed to rehabilitate after Mr. Christie canceled the construction of a rail tunnel beneath the Hudson River in 2010 and claimed billions in planned spending to be New Jersey’s money.

The prospect of reform is particularly urgent, according to the review, given the increasing burden posed by the PATH rail system. In 2012, the system lost about $400 million, according to data compiled by the authors, more than twice its loss in 2000.

The report estimated that between 2002 and 2020, the agency will have put more than $4.6 billion into the PATH system, and that excludes more than $1 billion in spending on a new PATH station at the World Trade Center. “It is no longer possible for the Port Authority to adequately fund its own facilities and services while simultaneously allocating hundreds of millions for non-revenue-generating state projects,” wrote the report’s authors, Mitchell Moss, the Rudin Center’s director, and Hugh O’Neill, a former assistant executive director at the Port Authority.

The report essentially follows these threads of argument deeper. The zero-return issue is a big problem, and one that strong leaders will have to tackle by defying the governors who appoint them. I doubt we’ll see too much movement in that regard any time soon.

But let’s look at the PATH problem. The PATH system should be one of the Port Authority’s bigger focuses. Unless PATH is somehow integrated into the MTA — a politically challenging move to say the least — it remains an important part of the Port Authority portfolio, but unlike the MTA, PATH is funded only through tolls and other PA revenue. As the report notes, “PATH is today the only major rail transit system in the U.S. that is funded entirely through a combination of farebox revenues and subsidies from other transportation facilities, without any support from broader-based tax revenues.”

That’s all well and good for PATH, but the taxes that fund the MTA, for instance, a key revenue driver. Without them, fares would be impossibly high or service highly inadequate. As Moss and O’Neill note, that could be PATH’s fate: “Without some broader base of support, the next decade is likely to see continued escalation of bridge and tunnel tolls and PATH fares, increased pressure to cannibalize revenues from other Port Authority businesses to further subsidize PATH, sharp reductions in service – or some combination of all three.”

Instead of bolstering what the report calls reliable, low-cost, trans-Hudson rail service that has fed Jersey City’s rebirth and Lower Manhattan’s recovery, the Port Authority has become mired in zero-return investments that New York and New Jersey Governors have pushed. It’s an unsustainable business model for the PA and one that has ramifications that extend well beyond the Port Authority’s little fiefdoms. Somehow it needs to change, but I’m not optimistic it will.

While I was out of town last week, Port Authority David Samson finally took one for the team as he resigned amidst the prolonged fallout over the Fort Lee traffic scandal. While driving across those very same lanes on Sunday night, I laughed about how those few miles of road leading to the George Washington Bridge could create such shockwaves both in New Jersey and on a national scale for politicians with ambitious that, at one point, extended well beyond Trenton.

The national politics are neither here nor there right now. Samson left without saying much more than two sentences: “Over the past months, I have shared with the governor my desire to conclude my service to the PANYNJ. The timing is now right, and I am confident that the governor will put new leadership in place to address the many challenges ahead.” Now, calls for reform are on the table, but will two governors who haven’t expressed much of a willingness to take on transit causes look to improve the Port Authority or simply aim to re-entrench their patrons in positions long known for patronage?

In the aftermath of Samson’s resignation, the Garden State’s governor said he is open to change. “I don’t think there’s any question that structural changes are a possibility,” Cuomo said. “It’s also very complex, because the entire legal and financing mechanism that exists has an asset base that is now a bistate asset base. So it’s much easier said than done.”

On the New York side, Gov. Andrew Cuomo has tried to circumvent the issue by directing state funds toward projects that were ostensibly under the Port Authority purview. Fed up with the pace of work at JFK and Laguardia, Cuomo has tried to reinsert the state in the planning picture. That’s a recipe for short-term progress but not for a long-term structural overhaul.

So where does the PA go from here? It won’t be easy to untangle a 93-year-old governing body that commands the area’s airports, a subway system, one of the largest development sites in the city and various bridges, but it may be worth a try. Here’s WNYC’s Kate Hinds toying with the idea:

At his press conference Friday, Gov. Christie said competing state politics lay at the heart of recent problems with the Port Authority of New York and New Jersey. Citing “a history of conflict between these folks at the Port Authority,” Christie said that the way to resolve the feud between the states was “taking the Hatfields and McCoys and moving them to separate homes. Because they haven’t been able to get along with each other, despite my best efforts, the best efforts of Governor Cuomo, and many of our predecessors.”

What he meant was converting the Port Authority from a bi-state operation into separate state agencies. Until today, Christie has blocked reform at the Port, while staffing it with political appointees who had no transportation experience. But what if he got his way and the authority were to be broken up?

The first task would be to untangle multiple bi-state facilities. The Port Authority oversees the region’s airports and interstate bridges and tunnels, not to mention the PATH trains, World Trade Center redevelopment, and… the ports. Its annual operating budget is $8.2 billion — and it has a ten-year, $27.6 billion capital plan. Transportation experts told TN that unwinding those co-owned assets would be a daunting task that probably should not be undertaken.

As Hinds — along with various regional transit and transportation experts — notes, breaking up the Port Authority is throwing out the baby along with the bathwater. Pointing to various other metropolitan regions with competing authorities, most experts seem to believe the blame lies not in the structure but at the top. “Breaking it up isn’t going to solve the problem,” City College professor Robert Paaswell said. “Managing it better will solve the problem.”

Can this agency be better managed? Can we get to a point where a tit-for-tat doesn’t involve a $1 billion investment at Ground Zero in exchange for a $1 billion PATH airport extension? Can two states with divergent political whims work together competently to improve the region’s transportation infrastructure? The answer has to be yes for the region to grow and Port Authority to succeed, but the current leadership hasn’t inspired much hope yet.