Transit advocates say that while they understand the angst over another fare increase, they are focused on securing money from state and city officials for the authority’s capital plan, which includes many of the very upgrades that would bring meaningful improvement to commutes. The plan proposes $32 billion in spending over five years, but it is $15 billion short — the largest funding gap ever and a striking sign of the difference between what the system needs and what the authority can afford.

Mr. Cuomo, a Democrat, has called the plan “bloated” and has not addressed the funding gap, instead publicly drawing attention to other infrastructure projects, including a new Tappan Zee Bridge and his proposal for an AirTrain to La Guardia Airport. But the authority’s chairman, Thomas F. Prendergast, has argued that the measures outlined in the capital plan are essential, such as replacing aging cars and tracks, modernizing the signal system so more trains can run and beginning the next phase of the Second Avenue subway.

For most riders, their only regular connection to the agency’s budget is the money they load onto their MetroCards. While some believe the authority makes a profit by charging more than the ride costs, the system is, in fact, heavily subsidized, with fares making up about 40 percent of its operating revenue. Experts have called for a more sustainable source of funding; one proposal, by Move NY, would establish tolls for drivers on the East River bridges in Manhattan, an idea that was rejected in Albany in 2008.

The most recent transportation authority statistics reveal that train delays increased in 2014, and new figures for January and February will probably reflect worsening delays, Mr. Ortiz said.

One metric called “wait assessment” — essentially whether trains arrive at platforms on time — decreased by 1.5 percent across the system in 2014 compared with 2013, and long gaps in time between trains rose to 6.4 percent, from 3.9 percent. Officials attributed the delays over the last year to several factors: an increase in track work, much of it in response to Hurricane Sandy; more aggressive track inspections; and safety slowdowns through work areas.

Mr. Ortiz attributed the recent uptick in delays this year to snow and low temperatures that caused rails to break and ice over, but transit advocates say the subway should be able to handle Northeast winters.