One advantage of the way MetroCard is designed is you can swipe your card as you walk through the turnstile, allowing large groups of people to move through quickly once they know to have their card out and ready (which you learn quickly, even a visitor to the city like myself)
Do we really want people fumbling with their phones trying to Touch ID to go through the turnstile? This will slow things down quite a bit compared to the current system.
A plain NFC card is fine. Requiring people to unlock their phones with TouchID (or even worse, FaceID) will slow down the crowds too much.
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I know, right? I don't even live there; I just visit, and I rarely have issues with Metrocards. You learn how to walk-and-swipe fairly quickly, at least in my experience.