I enjoy your map for the considerations, formula, and objectives set as your goal. The contrast of heavy and light lines suggest something different than local or express but I think as a rider I would then understand after one mistake or taking a bit more time to read the map.
There are a couple of items missing in your map that would help provide any vision-abled reader to use it:
More contrast for the boroughs; I did not see them clearly nor did I understand the boundary of regions. Previous maps illustrating landmarks such as bridges, rivers, and islands help a rider to understand based on what is known — Manhattan is an island.
There is a connection to Staten Island from Manhattan—some riders will be missing that connection because there is no indication of a ferry line.
As other commentors have mentioned, streets provide great landmarks for current location or destination. I want to get to a 86th street on 5th avenue; I would not know how to get there with this map.
I being familiar with the city know where Central Park is, but the vague patch of green does not indicate with immediate recognition that this is a park.
The current and previous maps provided a clear icon for transfer stations — a white bulbed line connecting the subway lines. Within your map, the adjacent subway line markers at stops did not indicate that clearly with great confidence; and the long connecting transfers were held together with a line too thin and hidden to indicate connections
The shape of the paths helped provide connection remarking the flow and geographical direction with out the slightly more complex organic paths of the current map. There is one map that changes the entire contextual relationship and that is Max Roberts render http://gothamist.com/2013/07/25/fun_map_nyc_subway_map_as_a_circle.php that still uses waterways indicating natural boundaries and landmarks. The map still provides a clear previous knowledge use of connecting station icons and keeps each station cleanly on a horizontal line. The concentric circle grid helps for a faster flow without causing too many quick lines and angled directions breaking a connection from beginning to end. However, I would still criticize this map for the lack of streets for subway context and the park name missing.
Still an awesome study that required a lot of data organization, research and skill which this effort should not go unrecognized.