The only level crossing where another train might occupy the tracks is Queens-bound from the JMZ stop at Myrtle Ave & Broadway in Brooklyn. The M crosses at grade over the J/Z track.
Most likely its not a technical challenge its a bureaucratic problem. Not to mention the unions aren't going to let the transit authority obsolete their jobs.
Living in New York, the amazing thing about the subway system is how they keep it running. It's old and ridiculously complex, and despite what natives say, the MTA by and large does a good job running it. There's no political will to fix it right now. It's going to take trains becoming unsafe or costing so much to keep safe that people eventually notice and start making noise about it, I think.
And I'm not talking just the technology - they have 31 billion dollars of debt to service, and constantly get the shaft from Albany when it comes to funding. They continue to take on debt because they have mandated projects and lack the funding to complete them.
My city's subway/elevated train system will be 30 years old this December. Train control is fully automated; there are no drivers on trains, and in normal operation there is no remote (human) operator either. It's been automated for 30 years. https://en.wikipedia.org/wiki/SkyTrain_(Vancouver)
(Side note: during the BART strike, some HN commenters suggested computers to replace drivers, and other commenters said that wouldn't be safe. Such hilarious technophobia on HN.)
I don't want to trivialize NYC's challenges and accomplishments: for one thing their system is far, far more complicated (468 stations on 34 lines, vs 47 stations on 3 lines), and for another we all know it's very hard to upgrade legacy systems.
But I'm astonished that they would work so hard to modernize their 1930s technology to 1970s standards in the 2010s.