Utilize expresses
This one may seem obvious, but it definitely merits emphasizing. You will shave minutes, even hours, off your travel time if you unlock the power of express trains. Check out the MTA subway map and take a look at all of the dots that mark each stop. The white dots are stations where the express lines stop. Need to go all the way from 125th to FiDi? Your phone will probably tell you to hop an E train. But you know better than that! Catch the A and watch all of the local stops whiz by you, because you know exactly what you're doing.
[Photo via @mta_subways]