The does not need to stop at 49th Street; in fact it shouldn't. The TA has said that rush hour crowds at 49th Street justify this, but having used 49th Street myself, I find their reasoning dubious. They just don't feel like performing the necessary switch/signal adjustment work, same way that they have still not gotten around to correcting the Montague clearance problem.
They also need to stop kidding themselves that Second Avenue will be ready to open before the end of the year (they've shifted the opening date to December 31st now). Considering the pace of their progress and the issues with 72nd and 86th Street, they should just come clean and admit the line won't be ready until at least February. Otherwise they'll have a situation like with 34th Street- sloppy work performed in such a rush that the ceiling leaked, escalators broke down after a few days and the second station entrance is still under construction.