Well, the subway system predates the Standards Manual by about 70 to 100 years (depends if you count the system from the first trains or its first underground section)...so it's wrong to infer that too many resources were devoted to the visual design rather than logistics and construction of the system over the decades. The system is complicated and convoluted because of both its age and its coverage. Certainly, the signage could be better in some places...is there a better way to sort out the mess in the midtown stations (Times Square, Herald Square, etc)? Sure...but those stations connect so many routes and other systems that some confusion will be inherent.
Combine that with a bureaucratic nightmare and not much gets done to fix issues or improve obvious areas. I remember recently reading about the amount of trash on the tracks and it was because antiquated equipment and horrid procurement processes topped off by some really annoying work rules.
