The Tel Aviv - Jerusalem train is actually being built and should be ready in 2 years or so.
There are talks about the E concourse for a while now but I can't see the real reason for it. There is no shortage of gates at TLV at any time during the day.
If anything is urgently needed in TLV it is a revamp and extension of the check-in area!
The main plan for changing the runways is to extend runway 03-21 to the north and make it the main arrivals runway. Nowadays, this runway is rarely used as a runway and is mainly used as the taxiway to runway 26 ("the quiet" one).