This winter's snows demonstrated the shortcomings of the Massachusetts Bay Transportation Authority.

Complaints about Boston's public transit system are nothing new — they're immortalized in a 66-year-old folk song — but they've taken a much sharper tone this winter when the system spectacularly failed its users under the weight of more than 100 inches of snow.

The lead character in the song "M.T.A." rode the subway eternally because of a fare dispute; but this winter Charlie's train probably wouldn't have arrived, leaving him stuck with his fellow Bostonians on a freezing platform or stalled between stations on a broken-down Red Line train.

The snow and deep freeze that pummeled Massachusetts did more than incapacitate the Massachusetts Bay Transportation Authority. It pushed an embarrassed agency, which operates the nation's oldest underground subway, plus streetcar and bus lines, several commuter rail lines and other entities, into a harsh national glare, along with the Massachusetts government.

The MBTA, including its commuter-rail subcontractor, French company Keolis, have been restoring service in pieces. Normal service across all lines isn't expected until sometime in March. Keolis has targeted March 30, the company said Thursday after its executives met with Gov. Charlie Baker and other top state officials.

"They had some serious issues to start with," said Joshua Schank, president and chief executive of the Washington think tank Eno Center for Transportation. "They have a very old system and a huge maintenance backlog — even bigger on a per-mile basis than what New York has — and years of neglect due to underfunding, long before the snowstorms."

Challenges include $19 billion of debt, some dumped onto the system as part of a mitigation settlement related to the Big Dig Central Artery/Tunnel highway project; a $5 billion maintenance backlog and train rolling stock on some lines so antiquated that "not even God Jr." could run them well, in the words of departing general manager Beverly Scott; and union work rules that are anathema to reformers.

The winter fiasco has prompted all sorts of suggestions for how to put Humpty Dumpty together again.

They range from calls for better funding of transportation infrastructure to a more draconian remedy, receivership, which Boston free-market think tank Pioneer Institute advocates. Under the latter, a different Charlie — Gov. Baker — would appoint an independent entity to run it.

According to Pioneer research director Greg Sullivan, Baker could cut through red tape and streamline work rules, the overhaul of which Sullivan likened to a "Tong War."

The MBTA — or the "T," as locals call it — has operated as a state Department of Transportation unit since 2009.

Sullivan said getting MBTA staff to even chart maintenance under National Transportation Safety Board best-practices guidelines is an adventure.

"I talked to the T bus maintenance chief and he said 'well, it's a union thing,' " said Sullivan. "It's a very expensive system to run. The salaries are high, the overtime is high, the number of people working on it is high and the rules are arcane."

In addition, he said, state laws have restricted the ability to outsource work — for instance, a private company must pay the same benefits as a state entity.

"We're not proposing violating any collective bargaining agreements, but the work rules required to maintain the system are very archaic," said Sullivan.

Baker, a Republican who took office in January, didn't speak with Scott until the situation reached its early February nadir, which hurt the perception of the commonwealth's ability to manage a crisis. The MassDOT board in 2012 appointed Scott, former general manager of the Metropolitan Atlanta Rapid Transit Authority and a favorite of Baker's predecessor, Deval Patrick.

Scott resigned under pressure earlier in February. The MassDOT board on Wednesday named Frank DePaola, who oversaw the state highway system, as interim general manager effective March 4. Scott will remain until April 11 to assist in the transition.

"Beverly Scott was absolutely in a no-win situation," said Schank. "I don't blame her at all. I'm sure she didn't do everything perfectly, but she's well-known as a competent and likeable leader in Atlanta and elsewhere. I think it's good that she got out on her own terms."

Scott likened the return to normalcy to a "30-day war." Given Keolis' latest timetable, it's more like 60 days.

"Right now, the level of frustration is at a record high, without a doubt. People are upset with the lack of preparedness," said Sullivan. "The response to the storm is way too slow. They didn't respond quickly enough. They didn't run the trains all night to keep the tracks clean. The switches froze; they were covered with ice."

According to Sullivan, a 17-year former lawmaker and former state inspector general, the MBTA's $6.2 billion capital plan for 2015-2019 included merely $2.8 million, or 1/20th of 1%, for snow-fighting equipment.

Sullivan, who culled statistics from the National Transit Database, said the MBTA was the only one of 18 commuter rail transit systems in the U.S. to post a net decline in annual passenger trips, a drop of 5.3 million per year, or 13%, from 2003 through 2013.

Keolis has operated the T's commuter trains since July after winning a $2.7 billion, eight-year contract to take them over from the Massachusetts Bay Commuter Railroad Co.

 As rumors swirled midweek about a change in commuter rail leadership at Keolis, the Boston Herald reported that the chief mechanical officer's slot at the company has remained vacant since August.

"The T has to focus on essential maintenance and get out of expansion mode," Sullivan said.

 The T over the past decade expanded its commuter and subway lines, including a Green Line streetcar system extension into Somerville, required under the Big Dig mitigation settlement.

Sullivan also questioned the recent purchase of rail rights between Boston and Foxborough, home of the New England Patriots' Gillette Stadium, from the CSX freight railroad. Massachusetts will spend $23 million to buy the line and millions more on track upgrades and equipment.

In addition, the unfunded liability related to the T's retirement plan has worsened, according to Pioneer senior fellow for finance Iliya Atanasov. It spiked from $111 million in 2008, when it was 94% funded, to $855 million in 2012, the last year for which data was available. The drop is 31 points, to 63% funded.

In transit, a tug of war exists between the lure of shiny, new stations — trophies to political and transit leaders — and the need for down-and-dirty maintenance, which federal regulations categorize as "state of good repair."

Schank said receivership for the MBTA isn't necessary. "Receivership's a bit extreme," he said. "They still have a funding source and the state is still financially healthy enough to back the MBTA."

The T now receives 20% of state sales tax revenue, which covers for almost half of its annual operating expenses. Fare collections and assessments from 175 communities the T serves also feed the system. The communities now share the roughly $156 million assessment using a population formula, according to Eno Center.

Eno's report last fall, "Getting to the Route of It," which examined Boston and several other regional transit systems, said it's "too politically challenging, and not worth the effort," to approach municipalities to pony up more of the system's cost. However, the shrinking contribution — in real terms — has left them with much less influence over MBTA decision-making.

Red Line subway expansion has included Cambridge in recent years but according to Schank, city officials cite increasing demand for bus service instead. "Cambridge wants a lot more buses but they can't get the MBTA to do that," he said.

Moody's Investors Service last April assigned an Aa2 rating to the MBTA's senior sales tax bonds, citing a commonwealth-guaranteed floor on sales taxes that protects bondholders. "We will continue to monitor the MBTA's operations," said Moody's. "Failure to resolve the authority's current operating challenges could exert further downward pressure on the rating."

Transit advocates say up to $1 billion over 10 years was lost when voters in November negated automatic increases in the state gas tax, indexed to inflation.

Baker, now front and center on the MBTA issue without Scott as a shield, formed a committee recently to examine overhaul of the agency. The governor said the panel will review performance and examine core functions at the T and benchmark results with other transit operations in governance, finances and capital planning.

But controversy even engulfed that move. Former Boston Redevelopment Authority director Paul Barrett resigned as panel chairman Friday night after the Boston Globe reported that Barrett's financial problems included nearly $200,000 in federal tax debt. Massachusetts Port Authority executive Brian McMorrow and Harvard University administrator Katie Lapp, former chief executive of New York's Metropolitan Transportation Authority, will co-chair the now six-member panel.

Notably missing from the panel is Fred Salvucci, widely respected in transit circles. As the state transportation secretary under then-Gov. Michael Dukakis — who rode the T to work — Salvucci helped keep the Boston subways running during the infamous 1978 blizzard.

The MassDOT board, meanwhile, will review fare reimbursement options in March. "A number of questions have been raised regarding fare reimbursement, including a range of suggestions," said Scott.

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