The Port Authority on Thursday approved a capital plan that includes funding toward building a new midtown bus terminal—but many questions linger about a replacement facility and the larger fate of the cross-Hudson commute.

The agency’s commissioners voted unanimously to pass the $32 billion program, a 10-year spending outline that allocates $3.5 billion to help replace the aging midtown bus terminal in Hell’s Kitchen. The authority expects 337,000 daily commuters to utilize the bus terminal by 2040, an increase of almost 47% from ridership levels today.

John Degnan, Port Authority chairman, considered the vote an important step in the facility’s proper design and planning process.

“I’m very pleased, as you can probably tell, that we’re finally moving ahead with this capital plan and specifically the plan for the bus terminal, which is a critical project—everyone acknowledges—for both New York and New Jersey residents,” Degnan said. “This work must begin as soon as possible to ensure we’re responding to the needs being created by the aging terminal and an increase in demand.”

But that $3.5 billion will not cover the complete cost to replace the 66-year-old terminal—the tab for the entire project has been estimated to be upward of $10 billion.

To move the preliminary work along, the Port Authority also approved Thursday the spending of $70 million for planning and permitting processes in the area. The agency will be moving ahead on the West Side location in hopes to win over the New York lawmakers, residents and other officials who oppose building a new terminal in the area over fears of increased congestion and the potential use of eminent domain.

The nasty clash between elected officials in New York and New Jersey over the project in the past few months had grounded the planning process to a halt.

The behavior “underscores the Hatfield and McCoy nature of how this agency operates,” said John Wisniewski, a New Jersey assemblyman and candidate for governor. “If we can’t solve that, then maybe we ought to seriously start thinking about unwinding this agency because having each state fend for itself is no different than what’s happening now.”

Transit experts believe the debate over the bus terminal is indicative of a larger problem with what they describe as a mismanaged Port Authority that has focused on flashy mega projects rather than the critically important infrastructure improvements.

Veronica Vanterpool, the executive director at the Tri-State Transportation Campaign and MTA board member, criticized the plan’s prioritization of airport access in both states, when she said money could be spent more wisely on mass transit projects that would affect a greater number of people, like the bus terminal, PATH service and the Gateway Program—the $23.9 billion project to repair and replace the 106-year-old tunnels under the Hudson that were badly damaged by Superstorm Sandy.

“There’s not enough attention being paid to that trans-Hudson commute…the real problem here is that there is no real focus on regional coordination,” said Vanterpool. “Projects are moving forward to appeal to individual state priorities as opposed to improving the commute in two states.”

Some $2.7 billion is allocated in the plan for Gateway. There’s also $2.5 billion allocated for two signature projects of Gov. Andrew Cuomo: the redevelopment of JFK and the building of an AirTrain to LaGuardia. One board commissioner, Ken Lipper, described the latter project last month as “amongst the most ill-conceived projects that I’ve experienced in government.”

Even with the $70 million bus terminal planning efforts taking shape, roadblocks could still lie ahead. Christine Berthet, of Community Board 4, advised the board to build multiple terminals on the west side and elsewhere. Hell’s Kitchen couldn’t bear the full weight of one massive terminal, she argued.

“We believe this narrow focus is short-sided and may very well delay the project, which everybody is very anxious to get done,” she said.