There has from the begining been alot of political postering over whether or not the twin towers could be reconstructed and that reconstruction solve the engineering issues that some think contributed to its collapse.
Some think it could only be done in a way where the outside appearance resembled the original but the structural elements were built differently.
Some, thought(a)that construction on a replacement could begin outside the original footprint sooner than the original footprint would be ready for construction (wrong - ignored how much politics would delay construction), (b) yet, there is not/was not likely to be sufficient area outside of the original footprint for two towers equal to the orignal.
Thus, no one could find sufficient agreement with sufficient numbers of other people on a process that would result in rebuilding the towers, because too many other people did not want to even consider rebuilding them.
Why is there such concern for the footprints? There is no footprint where the Pentagon was hit.
Doesn't look like the Murrah building has a footprint either
http://www.oklahomacitynationalmemorial.org/hist.htm