I'll address a few other points, including the IRT:
1) IRT Lexington Avenue Line
As it is, three lines are enough to pack the tracks to capacity. Adding a fourth line would be a logistical nightmare.
2) IRT Broadway/Seventh Avenue Line
The situation is not as desperate on this line as the Lexington Avenue Line, but the tracks are nearly packed to capacity. Adding a fourth line would be a logistical nightmare.
3) BMT Broadway Line
Unless I'm reading the map incorrectly, this line is cut from four lines to two. This would lead to hopeless overcrowding on the two remaining lines.
4) BMT Jamaica Line/Nassau Street
A lot of Queens customers on the line will complain about having to transfer in order to reach Manhattan.