I am hazy on the Born-Oppenheimer Approximation (BOA) and how that effects the QTAIM calculations and their interpretation. I am interested in real spaces instead of Hilbert spaces, I do not like the BOA approach, and the chemist’s Homo-Lumo etc…..
Of course, it is prejudice, that electrons follow nuclei or move independently. Some years ago I saw in Chem. Phys. Letters calculations of H2 molecule. Electrons and nuclei moved in opposite phases their. Unfortunately, I don't remember exact reference.
I believe that the good starting point would be the 2011 Chem. Rev. paper from Bartlett's group: http://pubs.acs.org/doi/abs/10.1021/cr2001417 and particularly the great comparison of the most accurate methods with all their advantages and disadvantages.
Some of the most accurate results for really small systems have been developed in the group of Ludwik Adamowicz from the University of Arizona; see his work in this topic.