In addition, the capital plan invests $2.75 billion to upgrade signals, including more than $1 billion earmarked for the computerized system known as communication-based train control, which allows cars to run closer together.

Still, some budget experts say that transit officials should have invested in computerized signals years ago.

“The mistake was the incredibly slow place at which they have approached upgrading and modernizing the signal system,” said Charles Brecher, director of research at the Citizens Budget Commission, an independent watchdog group. “What was spent on the Second Avenue subway could have paid for a lot of new signals.”

Veronique Hakim, interim executive director of the authority, insisted it had entered a new era of growth and renewal. “We spent the first 20 years of capital programs fixing decades of neglect in the transit system,” she said. “All of that changed dramatically.”

Others, including Mitchell L. Moss, a professor of urban policy and planning at New York University, and Gene Russianoff, the leader of the Straphangers Campaign rider advocacy group, agreed that modernizing the signal system should have been a priority in previous capital programs.

“When you’re talking about maintenance and improvements to such a massive and complex system as New York City Transit, trends develop over time and they are invisible to the riding public for years,” said Tom Wright, executive director of the Regional Plan Association, a nonprofit group.

“Then there’s more demand on the system, capacity is not increasing, maintenance is being stretched out,” he said. “And it doesn’t become visible until it hits a certain threshold level. That is what transit advocates expected to happen, and it’s what is happening now.”