I would like to see NE1 capable of handling the entire periodic table of elements. Support for interactions with photons could be added.
Does NE1 have threads to use multi-core systems? There is also the NE1 BOINC client that I do not think is currently being used. http://nanoengineer-1.com/nh1/
It has also been suggested to make 'save points' while a simulation is processing, so that it can resume a long computation if interrupted.