A few remarks, mostly in regard earlier posts.
First, the Bronx part of the Third Avenue El was torn down because it was originally built for wooden cars and couldn't take the weight of steel cars. In its last few years, it was serviced by R12's that had had the dynamic braking resistors torn off to reduce wieght, and the TA didn't want to eihter renovate the structure or buy lightweight cars that would be just for that line.
As to replacing the original Manhattan els, the 6th and 9th Avenues els were replaced by the 6th and 8th Avenue undergrounds as already explained. On the East Side, IMHO, the 2nd Avenue subway should be completed as promised, and a new 3rd Avenue would be good to have. Commenting realisitcally, I expect that Phase I of the Second Avenue will be completed between 2016 and 2020, and that Phase II has a moderate chance of eventually being built. However, I see a high risk that the southern half of a full Second Avenue line will again be deferred indefinitely based on financial considerations and that a new Third Avenue line will just remain an entry on a railfan's fantasy map.