The resignation Thursday of subways chief Andy Byford made an already grim 2020 picture even bleaker. The state-run Metropolitan Transportation Authority tried valiantly to put a positive spin on it, but it’s a sign that one of the world’s foremost experts on modernizing subways and buses thinks Gov. Andrew Cuomo doesn’t have the will to do it right.

When Byford joined the MTA two years ago, the subways were at their lowest point in modern history. In 2017, fewer than two-thirds of trains were on time; nearly 70 “major incidents” per month delayed hundreds of thousands of passengers.

Last year, as the MTA announced this week, 80 percent of trains were on time, and the number of “major incidents” each month was down to 46.

Byford had a big role in this turnaround, directing critically needed signal and track repairs. As MTA chief Pat Foye acknowledged, “Andy was instrumental in moving the system forward.”

But the MTA is hardly fixed. Eighty percent on-time performance isn’t stellar: 34,000 trains are still delayed each month. Over two years, the MTA has spent billions of taxpayer dollars simply getting the MTA to a semi-acceptable state of service, where it should have been if it weren’t for neglect of basic maintenance that started early during Cuomo’s tenure.

The MTA never used Byford as well as it could have. It essentially shut him out of contract negotiations with the agency’s largest union, the Transport Workers Union, meaning he had little opportunity to bring the insight he had gained working at subways in other countries to make changes so that workers get more done on every shift, thus saving riders and taxpayers money.

But the real work is just starting. The MTA’s new $52 billion, five-year plan to invest in physical assets includes $7 billion to modernize subway signals. Right now, only two subway lines, the L and the 7, are digitized, and the work took much longer than it should have — more than a decade. For all that, the new signal system on the 7 train doesn’t work well in light snow.

Subway modernization was supposed to be Byford’s favorite project. He spent much of his first year running around town showing his signal modernization slideshow to anyone who would listen, pledging to modernize the signals on the 4, 5 and 6 lines, the system’s busiest, within five years, and to modernize nearly all signals within a decade. The fact that he left indicates that he thinks the MTA isn’t going to do this right.

The Legislature in Albany, which approved congestion pricing last year, thus enabling this work, should be worried: Is the MTA going to waste the first decade’s worth of congestion pricing revenue on a signal system that doesn’t work as well as it could?

Byford’s second-favorite project: buses. New York has been losing bus riders for a decade now, as people grow frustrated with the slow pace and cumbersome boarding process. The MTA is only now embarking on an ambitious plan to modernize routes. Byford, with his experience in London, famous for its efficient buses, could have increased ridership with new attention here, taking pressure off crowded subways and luring people from their cars in eastern Queens and Staten Island. Now, the risk is that buses are orphaned again.

Byford gave insular New York a fresh eye in other important ways, too. Longtime New Yorkers know it is a political no-no to point out that it’s not acceptable to have people — around 2,000, at last count — using the subway system as a homeless shelter and mental health institution. Byford, with experience in systems where people simply don’t live in the subway, wasn’t afraid to raise this topic.

So why is Byford leaving? The scuttlebutt will be that Cuomo didn’t like Byford taking credit for the subway’s turnaround. The reality may be worse: He may have come to believe that he couldn’t assert enough power to make it worth staying. He’s competing with too many others within an increasingly convoluted management.

No one is irreplaceable or should be — and Byford is not the only person in the world who understands how global subways are supposed to work. The question is: Since it’s obvious that he ran away from dysfunction under Cuomo, will any other global experts take a chance in Gotham?

New York is now flush with subway cash, thanks to taxpayers, riders and (soon) drivers — but with no one qualified to spend it properly.

Nicole Gelinas is a contributing editor of City Journal. Twitter: @NicoleGelinas