It’s been three days since Mayor Bill de Blasio and Governor Andrew Cuomo announced their surprise deal on MTA capital funding, and we’ve all had enough time to declare Cuomo the winner. After months of bruising media battles, the city gave up more money in exchange for a hollow promise from the state to continue to follow a toothless law. Despite his rhetoric on affordable housing, De Blasio hasn’t embraced transit as a cause, and it showed.

For now, though, that’s neither here nor there. The state and the city still have to identify funding sources, and claims that no new taxes or fees will be implemented to generate $9 billion from the state seems laughable. The resistance to a rational plan to cut Manhattan congestion and generate transit revenue is almost as absurd as the fight between the mayor and governor over funding splits. But there’s another problem that now comes to the forefront and that problem is cost.

During the debate over funding responsibilities, the discussion on costs often took a backseat. The usual crew of transit advocates in New York City aren’t too keen to press on costs. They’re content to fight for dollars without questioning whether those dollars are being spent appropriately or efficiently, and as a sweeping generalization, few people would claim they are. Do the MTA’s costs make sense? No, of course not. Is anyone willing to do anything about it? Not yet.

The MTA’s high capital costs — and, to a lesser degree, operating costs — is a topic I’ve covered before, most recently in April when Dana Rubinstein reported that most transit organizations in New York City relied upon Alon Levy’s work to discuss high costs. This isn’t to say Alon’s work isn’t worthwhile; as I said then and reiterate now, it’s the most thorough examination of New York City’s high costs that exists in the transit sphere. His 2011 examination of ongoing capital projects remains ever green, and even without the absurdly expensive Fulton St. Transit Center or WTC PATH hug, New York City is home to the three most expensive underground rail projects in the world on a per-kilometer basis. At $1.5 billion per kilometer, the 7 line extension wasn’t the most expensive because the Second Ave. Subway costs $200 million more per kilometer, and that’s not the most expensive because East Side Access costs nearly double that.

It’s time to figure out why. In her story earlier this year, Rubinstein blamed “labor costs, work rules, managerial incompetence, the spaghetti of infrastructure tangled beneath Manhattan’s streets, a political firmament without incentive to tackle hard issues.” She didn’t touch upon another issue — corruption — that few are willing to discuss on the record, but corruption too serves as a reason for New York City’s high costs. Is anyone willing to rein them all in?

At this point, with the MTA’s capital plan funded to the tune of nearly $30 billion when all is said and done, it’s hard to argue that the agency is underfunded. It certainly has a backlog of projects due to decades of deferred maintenance and can’t seem to get out of its own way with regards to technological improvements such as the widespread installation of countdown clocks or a fare payment system a bit more cutting edge than the late 1980s/early 1990s MetroCard system. But the agency now also has access to a ton of cash, and imagine just how far it could go if the Second Ave. Subway cost $600 million per kilometer — second on Alon’s list to London’s Crossrail project — rather than three times as much.

Taking on costs and the forces driving them up requires far more of a politically bruising fight than securing some funding. Everyone wanted the funding, but few of the recipients of the funding, especially those in the construction industry, want lower construction costs. But without some attempt at rationalizing MTA construction costs, we’ll never have the subway expansion we need or a modern system with bells and whistles New Yorkers enjoy in other cities. And that’s a battle that someone needs to fight.