Manhattan's topology gets really strange after about 106th street on the West Side. That's not an excuse in itself, but the fact that Manhattanville is lower than its surroundings on all sides makes for some interesting tunneling. Elevated lines (like the 1 after 116) are also a problem in terms of maintenance and noise/light pollution.

> because normal yellow cabs don't operate in Harlem, for reasons I still don't understand

This is an ugly relic of NY's more violent (and more explicitly racist) past. I went to school with the kids of cabbies, and anything past the UWS was essentially off limits thanks to 30 year old stereotypes about the people living there.