But a 2 inch rain in under one hour flooded the New York subway which doesn’t seem like much rain at all.

Let's calc Manhattan alone, for simplicity.

First we check the total amount of water pouring down over that area.

22.83 sq mi = 91,650,797,568 sq in
91,650,797,568 sq in * 2 inch rain = 183,301,595,136 cu in
183,301,595,136 cu in = 793,515,869 gal

Back to pumping: they pumped 15m gal but on a dry day they pump 10m gal, so the difference was 5m gal.

5,000,000 / 793,515,869 = 0.0063

So a mere 0.63% of the total (potential) 2 inches of rain that would fall across Manhattan was pumped out of the subway system. That's pretty impressive on its own - from a subway perspective, drainage is 99.37% effective under 2 inches of rain.

Of course, the efficiency will fall hard under 3 or 5 inches of rain, which is the real issue here. More extreme weather = margins getting smaller.